Modified rna with decreased immunostimulatory properties

ABSTRACT

The present invention provides a method for providing modified mRNAs of reduced immunogenicity and/or immunostimulatory capacity for use in protein replacement therapy. The invention further provides modified mRNAs and pharmaceutical compositions comprising the modified mRNAs according to the invention for use in protein replacement therapy.

This application is a continuation of U.S. application Ser. No.15/142,082, filed Apr. 29, 2016, which is a continuation ofInternational Application No. PCT/EP2014/002931, filed Oct. 31, 2014,which claims priority to International Application No.PCT/EP2013/003293, filed Nov. 1, 2013. The entire contents of each ofthe above referenced disclosures are specifically incorporated herein byreference.

FIELD OF THE INVENTION

The present invention relates to a method for providing an mRNA withdecreased immunostimulatory properties, which encodes at least onebiologically active polypeptide or protein and its use in proteinreplacement therapy.

BACKGROUND OF THE INVENTION

Therapeutic RNA molecules represent an emerging class of drugs.RNA-based therapeutics include messenger RNA (mRNA) molecules encodingantigens for use as vaccines. mRNA vaccines combine desirableimmunological properties with the flexibility of genetic vaccines. Oneof several advantages of using mRNA for vaccination is that the samemolecule not only provides an antigen source for the induction of anadaptive immune response, but can simultaneously bind to patternrecognition receptors such as Toll like receptors (TLRs) and therebystimulate innate immunity. It has previously been reported that atwo-component mRNA-based vaccine with dual activity induces balancedTLR-7 dependent adaptive immune responses and provides anti-tumoractivity (Fotin-Mleczek et al., 2011. J. Immunother. 34(1):1-15). Inaddition, mRNA is considered to be a safer vector than DNA-based vectorsbecause RNA cannot integrate into genomic DNA possibly leading toinsertional mutagenesis.

mRNA molecules may also be used as therapeutics for replacementtherapies, such as e.g. protein replacement therapies for substitutingmissing or mutated proteins such as growth factors or enzymes, inpatients. However, successful development of safe and efficaciousmRNA-based replacement therapies are based on different requirementscompared to vaccines. When applying mRNA for protein replacementtherapies, the mRNA should confer maximal expression of the protein ofinterest in terms of expression level and duration and minimalstimulation of the immune system to avoid general immune responses bythe patient to be treated and specific immune responses against theadministered mRNA molecule.

Whereas the inherent immunostimulatory property of mRNA is considered asa desirable feature for vaccines, this effect may cause undesiredcomplications in replacement therapies. This is especially the case forthe treatment of chronic diseases in which the mRNA therapeutic needs tobe administered repeatedly over an extended period of time to patients.Although it has been demonstrated in animal studies that mRNA-encodedgrowth factor erythropoietin (EPO) can be successfully expressed in vivoresulting in biologically relevant increases of reticulocytes (Schlakeet al., 2012. RNA Biol. 9(11):1319-30; Kariko et al., 2012. Mol. Ther.20(5):948-53; Kormann et al., 2011. Nat. Biotechnol. 29(2):154-7), ithas been recognized that the immunostimulating properties of the mRNAmay potentially give rise to issues during therapy. Accordingly, suchproperties should be decreased.

Mammalian cells harbor a diverse set of nucleic acid-sensing patternrecognition factors (PRRs) receptors that recognize RNA by variousrecognition patterns (Review: Desmet et al., 2012. Nat. Rev. lmmunol.12(7):479-91). Toll-like receptors (TLRs) are the best studied group ofpattern recognition factors (PRRs). Out of the 10 human TLRs four TLRs(TLR3, TLR7, TLR8 and TLR9) are nucleic acid sensors that recognizediverse pathogen-derived nucleic acids. Whereas TLR3, TLR7 and TLR8recognize RNA, TLR9 binds to CpG motifs in DNA. TLR3, TLR7, TLR8 andTLR9 are intracellular TLRs and recognize nucleic acids that are takenup by the cell via endocytosis and transferred to endosomes. With theexception of TLR3, all nucleic acid-sensing TLRs use the adaptor proteinMYD88 for downstream signaling to activate the transcription factors AP1and NF-κB leading to the expression of pro-inflammatory cytokines. Thesecytokines mediate the recruitment and activation of immune cells. TLR3signaling depends on the TIR-domain-containing adaptor protein inducingIFNβ (TRIF) leading to the expression of pro-inflammatory cytokines aswell as type I interferons (IFNs), which play a role in antiviralresponses. For example, following TLR7 and TLR9 activation, plasmacytoiddendritic cells (pDCs) can produce large amounts of type I interferons(Desmet et al., 2012. Nat. Rev. Immunol. 12(7):479-91).

RIG-I-like receptors (RLRs) are members of the DExD/H-box helicasesuperfamily that act as cytosolic RNA sensors. Members of this familyare retinoic acid-inducible gene I (RIG-I), melanomadifferentiation-associated protein 5 (MDA5) and laboratory of geneticsand physiology 2 (LGP2). RLRs are expressed broadly by immune andnon-immune cells. The typical natural ligand of RIG-I is a short RNAwith blunt-ended base-pairing and an uncapped 5′ triphosphate end, butRIG-I has also been shown to bind to various double-stranded RNA (dsRNA)and single-stranded RNA (ssRNA) ligands. MDA5 generally binds to longdsRNA molecules but is also involved in the discrimination of self andnon-self RNAs based on the ribose 2′-O-methylation status of the capstructure (Züst et al., 2011. Nat. Immunol. 12(2):137-43, PMID21217758). In addition, RIG-I and MDA5 can be activated by self RNAsthat are cleaved by RNAse L. RNase L is a ribonuclease that is inducedin response to type I interferons and degrades all the RNA within thecell. RLR signaling depends on the adaptor IFNB-promotor stimulator 1(IPS1) leading to the activation of transcription factors IRF1, IRF3,IRF7 and NF-κB and subsequently to the expression of type I IFNs andpro-inflammatory cytokines (Broz et al., 2013. Nat. Rev. Immunol.13(8):551-65).

2′-5′ oligoadenylate synthetases (OASs) and the protein kinase regulatedby RNA (PKR) are both interferon-induced, dsRNA-dependent enzymeslocated in the cytosol that play important roles in mediating theantiviral effects of the interferons. PKR is a protein serine/threoninekinase that acquires enzymatic activity following autophosphorylation, aprocess mediated by dsRNA. Activation of PKR allows the kinase tophosphorylate its natural substrate, the alpha subunit of eukaryoticprotein synthesis initiation factor-2 (EIF2-alpha), leading to theinhibition of protein synthesis. The 2′-5′ oligoadenylate synthetasesare also activated by dsRNA and subsequently polymerize ATP into2′-5′-linked oligoadenylates (2′-5′ (A)) of various lengths, whichfunction as specific activators of a latent endoribonuclease, RNase L.Once activated by 2′-5′ (A), RNase L degrades viral and cellular RNAsresulting in the inhibition of protein synthesis. Both enzymes, PKR and2′-5′ oligoadenylate synthetase, are activated by ssRNA and dsRNA thatpossess extensive secondary structure (Sharp et al., 1999. Virology257(2):303-13).

Accordingly, RNA molecules may exert an unspecific immune response inpatients, which should be avoided or at least reduced. Severalapproaches were described for decreasing the immunostimulatoryproperties of mRNA including the incorporation of naturally occurringmodified nucleosides into in vitro transcribed mRNA. The purification ofsuch mRNAs is expected to remove contaminants or double-stranded RNA.Alternatively, the synthesis and use of novel non-naturally occurringmodified nucleosides with decreased immunostimulatory potential wasenvisaged as well.

Kariko et al. demonstrated that different mRNAs stimulated the secretionof cytokines, such as TNFα, by human dendritic cells (DCs) to variousextents, an effect that was attributed to the engagement of TLR3, 7 and8 (Kariko et al., 2005. Immunity 23(2):165-75). Whereas synthetic dsRNA,in vitro transcribed RNA as well as bacterial and mitochondrial RNAinduced strong cytokine secretion, cytoplasmic RNA from mammalian cellsstimulated DCs to a much lower extent. In addition, it was shown thatRNA signals through human TLR3, TLR7, and TLR8. Incorporation ofmodified nucleosides such as 5-methylcytidine (m5C), N6-methyladenosine(m6A), 5-methyluridine (m5U), 2-thiouridine (s2U), or pseudouridine (ψ),however, ablated this activity. Dendritic cells (DCs) treated withmodified RNA expressed significantly less cytokines and activationmarkers than those treated with unmodified RNA. The authors concludedthat nucleoside modifications suppress the potential of RNA to activateDCs. Therefore, it was suggested that mRNAs containing naturallyoccurring modified nucleosides may be used in clinical applications dueto their reduced immunostimulating properties (Kariko et al., 2007.Curr. Opin. Drug Discov Devel. 10(5):523-32; WO2007024708A1).

Further work demonstrated that in vitro generated mRNA containinguridine activated RNA-dependent protein kinase (PKR), which thenphosphorylated translation initiation factor 2-alpha (elF-2α), andinhibited translation. In contrast, in vitro transcribed mRNAscontaining pseudouridine as a modified nucleoside activated PKR to alesser degree, while translation of pseudouridine-containing mRNAs wasnot repressed (Anderson et al., 2010. Nucleic Acids Res.38(17):5884-92).

In addition, the Kariko group showed that in vitro transcribed,unmodified RNA activates 2′-5′ oligoadenylate synthetase (OAS), inducedRNase L-mediated ribosomal RNA (rRNA) cleavage and was rapidly cleavedby RNase L. In contrast, RNA containing modified nucleosides activatedOAS less efficiently and induced limited rRNA cleavage, thus showing therole of nucleoside modifications in suppressing immune recognition ofRNA (Anderson et al., 2011. Nucleic Acids Res. 39(21):9329-38).

Purification of in vitro transcribed mRNA by high performance liquidchromatography (HPLC) has been shown to reduce immune activation bytransfected mRNA. It was reported that contaminants, including dsRNA, innucleoside-modified in vitro transcribed RNA were responsible for innateimmune activation and that their removal by high performance liquidchromatography (HPLC) resulted in mRNA that did not induce theproduction of IFNs and inflammatory cytokines. It was translated at 10-to 1000-fold greater levels in primary cells. Although unmodified mRNAswere translated significantly better following purification, they stillinduced significant levels of cytokine secretion (Kariko et al., 2011.Nucleic Acids Res. 39(21):e142).

Treatment of mice with pseudouridine modified mRNA coding forerythropoietin (EPO) gave rise to higher protein expression and strongerbiological effects compared to unmodified mRNA. Moreover, the modifiedRNA did not induce detectable levels of interferon a and anti-EPOantibodies in plasma. In addition, it was shown that intraperitonealinjection of EPO mRNA into macaques increased serum EPO levels (Karikoet al., Mol. Ther. 20(5):948-53).

By another study, using a combination of different nucleotidemodifications, enhanced expression and reduced immunostimulation of anEPO-encoding mRNA was demonstrated in mice. Furthermore, in a mousemodel of a lethal congenital lung disease caused by the lack ofsurfactant protein B (SP-B), the application of an aerosol of modifiedSP-B mRNA to the lung showed a therapeutic effect (Kormann et al., 2011.Nat. Biotechnol. 29(2):154-7; WO2011012316).

The induction of induced pluripotent stem cells (iPSCs) was reported bytransfection of human cells with synthetic modified mRNA. Improvedexpression and reduced immunostimulation, indicated by lower expressionof interferon-regulated genes, were observed with base-modified mRNAscontaining 5-methylcytidine and pseudouridine (Warren et al., 2010. CellStem Cell. 7(5):618-30; WO2011130624; WO2011071931).

WO2013/052523 reports novel modified nucleosides, nucleotides andnucleic acids which can exhibit a reduced innate immune response whenintroduced into cells. However, any approach to reduce innate immunestimulation based on an mRNA containing non-natural modified nucleosidesis less desired. Any such modification, which does not usually occur inpatients, bears the risk of undesired side effects.

In view of the above, there is a continued need for novel methods toreduce the immunostimulatory properties of mRNA while maintainingefficient protein expression and a good safety profile avoiding any riskof undesired side effects.

SUMMARY OF THE INVENTION

The present inventors have identified an appropriate method to modulate,preferably decrease, the immunogenicity and/or immunostimulatorycapacity of a target mRNA (immune response against an mRNA), whichencodes at least one biologically active polypeptide or protein, bypreferably increasing the cytosine-content (C-content) of the codingregion encoding the at least one biologically active polypeptide orprotein and optionally exchanging additionally relatively rare codons inthe target wild type sequence by relatively frequent codons that codefor the same amino acid.

According to a first embodiment, the method for targeted modulation,preferably reduction of the immune response against an mRNA coding forat least one biologically active polypeptide or protein of the presentinvention comprises the steps of identifying a target mRNA wild typesequence coding for the biologically active polypeptide or protein andmodifying said mRNA by replacing at least 70% of the codons of the wildtype sequence, which are “cytosine content optimizable”, by codons witha higher cytosine content, thereby increasing the cytosine-content ofthe mRNA such that the cytosine-content of the coding region of themodified mRNA (coding for the polypeptide or protein) is larger than thecytosine-content of the coding region of the wild type mRNA (coding forthe at least one polypeptide or protein), whereby the encoded amino acidsequence remains unchanged compared to the wild type (amino acid)sequence.

In a preferred embodiment of the present invention, the modified targetmRNA is modified such that at least 10%, 20%, 30%, 40%, 50%, 60%, 70% or80%, or at least 90% of the theoretically maximal cytosine-content oreven a maximal cytosine-content is achieved.

In further preferred embodiments, at least 10%, 20%, 30%, 40%, 50%, 60%,70%, 80%, 90% or even 100% of the codons of the target mRNA wild typesequence, which are “cytosine content optimizable” are replaced bycodons with a higher cytosine-content as present in the wild typesequence.

In a further preferred embodiment, some of the codons of the wild typecoding sequence may additionally be modified such that a codon for arelatively rare tRNA in the cell is exchanged by a codon for arelatively frequent tRNA in the cell, provided that the substitutedcodon for a relatively frequent tRNA carries the same amino acid as therelatively rare tRNA of the original wild type codon. Preferably, all ofthe codons for a relatively rare tRNA are replaced by a codon for arelatively frequent tRNA in the cell, except codons encoding aminoacids, which are exclusively encoded by codons not containing anycytosine, or except for glutamine (Gin), which is encoded by two codonseach containing the same number of cytosines.

In a further preferred embodiment of the present invention, the modifiedtarget mRNA is modified such that at least 80%, or at least 90%of thetheoretically maximal cytosine-content or even a maximalcytosine-content is achieved by means of codons, which code forrelatively frequent tRNAs in the cell, wherein the amino acid sequenceremains unchanged.

Accordingly, the above objects of the present invention are solved by amethod, which provides for a modified target mRNA encoding at least onebiologically active polypeptide or protein with decreased immunogenicityand/or immunostimulatory capacity compared to the wild type sequence,wherein the C-content of the coding region of the modified target mRNAis typically increased by at least 10%, preferably by at least 12.5%,more preferably by at least 15% based on the cytosine-content of thepolypeptide or protein coding region of the wild type mRNA.

In a specific embodiment, the present invention provides for a method,in which, additionally to the increase in cytosine-content, some codons,preferably all codons of the wild type sequence, which are notcytosine-content optimizable or which do not code for glutamine, andwhich reflect a relatively rare codon in the cell, are replaced bycodons, which code for a relatively frequent tRNA in the cell, whichcarries the same amino acid as the relatively rare tRNA.

Preferably, the codon adaptation index (CAI) of the region of theimmunologically modulated mRNA coding for the polypeptide or proteinaccording to the invention is increased by at least 0.05, preferably byat least 0.1, preferably by at least 0.125, most preferable by at least0.15 as compared to the CAI of the wild type coding region of the mRNAencoding for the polypeptide or protein. Accordingly, the modified mRNAdisplays preferably an increased level of expression compared to thewild type mRNA.

The method according to the present invention may further comprise thestep of assaying the immunogenicity and/or immunostimulatory capacity ofthe modified target mRNA coding for the at least one polypeptide orprotein. Preferably, the immunogenicity and/or immunostimulatorycapacity of the modified target mRNA encoding at least one biologicallyactive polypeptide or protein is assayed by transfecting peripheralblood monocytes (PBMCs) in vitro with the inventive modified targetmRNA, culturing the cells for at least 8 hours, preferably for at least12 hours, more preferably for at least 20 hours and determining theamount of pro-inflammatory cytokines in the cell supernatant. The resultof such an assay may be compared—in a further optional step—with theresult of parallel experiments carried out for the underlying wild type(wt) sequence.

According to the invention, the target mRNA coding for the at least onebiologically active polypeptide or protein of lower immunogenicityand/or immunostimulatory capacity compared to the wild type sequence isselected from all of the modified target mRNAs obtainable by a method ofthe invention. Optionally, the inventive method according to the aboveembodiments may be reiterated to further decrease the immunogenicityand/or immunostimulatory capacity of the target mRNA, which encodes atleast one biologically active polypeptide or protein. Accordingly,alternative modified target mRNAs exhibiting the structural propertiesof the invention may be produced and tested.

According to one embodiment of the present invention, the targetedmodulation of the immune response against an mRNA encoding at least onebiologically active polypeptide or protein is carried out by way ofexecuting at least one algorithm of the cytosine-optimization on acomputer with the aid of suitable software.

The present invention also provides for a modified mRNA of reducedimmunogenicity and/or immunostimulatory capacity encoding at least onebiologically active polypeptide or protein according to one or moreembodiments of the present invention, wherein the modified mRNA isobtained by means of chemical or biological synthesis. Preferably, themodified mRNA is obtained by in vitro transcription, preferably bybacteriophage polymerase-mediated in vitro transcription, e.g. by Sp6polymerase in vitro transcription and/or T3 polymerase-mediated in vitrotranscription, preferably by T7 polymerase-mediated in vitrotranscription.

The present invention also provides a modified mRNA of reducedimmunogenicity and/or immunostimulatory capacity encoding at least onebiologically active polypeptide or protein obtainable by methodsaccording to the invention.

In this context, it is particularly preferred that the modified mRNA ofreduced immunogenicity and/or immunostimulatory capacity encoding atleast one biologically active polypeptide or protein according to theinvention has at least 10%, 20% or at least 30% lower immunogenicityand/or immunostimulatory capacity as compared to the respective wildtype mRNA.

The modified mRNA of reduced immunogenicity and/or immunostimulatorycapacity according to the present invention is typically characterizedby a lower affinity, e.g. at least decreased by 20% to one or more, toTLR3, TLR7, TLR8, PKR, MDA5, RIG-I, LGP2 or 2′-5′-oligoadenylatesynthetase, as compared to the wild type mRNA encoding the at least onepolypeptide or protein.

Furthermore, the inventive modified mRNA according to one or more of theabove embodiments comprises a 5′ CAP structure, and/or at least one 3′-and/or 5′-UTR (untranslated region) and/or a polyA-tail of at least 60nucleotides, more preferably of at least 70 nucleotides and/or a 3′stabilizing sequence.

Accordingly, the present invention also provides a pharmaceuticalcomposition, which comprises a modified mRNA according to one or more ofthe above embodiments, which optionally comprises one or morepharmaceutically acceptable excipients, carriers, diluents and/orvehicles.

More specifically, the present invention provides a pharmaceuticalcomposition according to the above embodiment or the modified mRNAaccording to one or more of the above embodiments for use in thetreatment of protein replacement therapy, preferably for use in thetreatment of e.g. hereditary or endocrinological diseases.

Furthermore, the present invention provides a method of treating asubject in need of protein replacement therapy, the method comprisingadministering to a subject in need thereof a pharmaceutically effectiveamount of the pharmaceutical composition according to one or more of theabove embodiments or an effective amount of the modified mRNA accordingto one or more of the above embodiments.

More specifically, the present invention provides a method according tothe above embodiment, wherein the disease to be treated by proteinreplacement therapy is selected from the group consisting of hereditaryor endocrinological disorders, such as e.g. amino acid metabolismdisorders, carbohydrate metabolism disorders, cholesterol biosynthesisdisorders, fatty acid oxidation defects and fat metabolism disorders,lactic acidosis, glycogen storage diseases, mitochondrial disorders,organic acid disorders, urea cycle disorders, lysosomal storage diseasedisorders.

More preferably, the present invention provides a method for expressinga biologically active polypeptide or protein in a tissue in vivo, themethod comprising contacting the patient with a pharmaceuticalcomposition according to one or more of the above embodiments of theinvention, or contacting the patient with the inventive modified mRNAaccording to any one of the above embodiments of the invention, whereinadministering the pharmaceutical composition or the modified mRNAresults in a reduced innate immune response by the patient relative to apatient, preferably the same patient, contacted with the wild type mRNAmolecule encoding the same polypeptide or protein. Optionally, the levelof mRNA expression in vivo is increased by the modified target mRNA ofthe invention as compared to the wild type mRNA.

According to a further embodiment, the present invention provides for amodified mRNA that codes for at least one biologically activepolypeptide or protein, wherein the cytosine-content of the codingregion of the modified mRNA is larger than the cytosine-content of thecoding region of the wild type mRNA coding for the polypeptide orprotein, whereby the encoded amino acid sequence is unchanged comparedto the wild type sequence. In this context, it is preferred that, if nocytosine is present in any of the at least one codon coding for theamino acid, at least one codon of the wild type sequence that codes fora relatively rare tRNA in the cell is exchanged for a codon that codesfor a relatively frequent tRNA in the cell that carries the same aminoacid as the relatively rare tRNA.

BRIEF DESCRIPTION OF THE DRAWINGS

The present invention is described by the figures and examples below,which are used only for illustration purposes and are not meant to limitthe scope of the invention. Owing to the description and examples,further embodiments are likewise included in the invention that areaccessible to the skilled person.

FIG. 1: Wildtype mRNA sequence R873 coding for Photinus pyralisluciferase (PpLuc), which corresponds to SEQ ID NO:1. The mRNA was invitro transcribed from a vector containing a T7 promoter followed by asequence coding for Photinus pyralis luciferase (PpLuc(wt), and apoly(A) sequence of 70 adenosine nucleotides (A70). This sequence wassubsequently used as a target sequence for modulating the immunogenicityand/or immunostimulatory capacity according to the inventive method.

FIG. 2: G/C-enriched mRNA sequence R875 which is obtained by G/Cenrichment only coding for Photinus pyralis luciferase (PpLuc), whichcorresponds to SEQ ID NO:2. R875 was obtained by G/C enrichment of thesequence R873.

FIG. 3: C-enriched mRNA sequence R2103 obtained by G/C enrichment andsubsequent C-enrichment coding for Photinus pyralis luciferase (PpLuc),which corresponds to SEQ ID NO: 3. R2103 was obtained by C-enrichment ofthe sequence R873.

FIG. 4: G/C-enriched mRNA sequence R2349 coding for Photinus pyralisluciferase

(PpLuc), corresponding to SEQ ID NO:4. The mRNA was in vitro transcribedfrom a vector containing a T7 promoter followed by a G/C-enrichedsequence coding for Photinus pyralis luciferase (PpLuc(GC)III) and asequence of 64 adenosine nucleotides (A64) poly(A) sequence.

FIG. 5: C-enriched mRNA sequence of R2350 coding for Photinus pyralisluciferase (PpLuc), which corresponds to SEQ ID NO:5. The template forin vitro transription was obtained by modifying the vector comprisingthe G/C-enriched sequence by replacing the GC-optimized coding sequenceof PpLuc(GC)III (FIG. 4) by a C-enriched sequence. mRNA obtained fromthis vector by in vitro transcription is designated “PpLuc(GC)III-A64”(R2350).

FIG. 6: G/C-enriched mRNA sequence R2791 coding for Photinus pyralisluciferase (PpLuc), corresponding to SEQ ID NO:6. The vector used for invitro transcription comprised a 5′-TOP-UTR derived from the ribosomalprotein 32L, followed by a stabilizing sequence derived from thealbumin-3′-UTR, a stretch of 64 adenosine nucleotides(poly(A)-sequence), a stretch of 30 cytosines (poly(C)-sequence), and ahistone stem loop.

FIG. 7: C-enriched mRNA sequence of R2793 coding for Photinus pyralisluciferase (PpLuc), corresponding to SEQ ID NO:7. The vector used for invitro transcription comprises a 5′-TOP-UTR derived from the ribosomalprotein 32L, followed by a stabilizing sequence derived from thealbumin-3′-UTR, a stretch of 64 adenosines (poly(A)-sequence), a stretchof 30 cytosines (poly(C)-sequence), and a histone stem loop.

FIG. 8: TNFα secretion of PBMCs treated with R2793 and R2791 mRNAs.

-   -   Human PBMCs were treated with 10 μg/ml of GC- or C-enriched mRNA        for 20 hours and the TNFα concentration was determined in the        supernatant by ELISA as described in Example 2.    -   As can be seen, the treatment with C-enriched mRNA (R2793)        results in significantly less TNFα secretion than treatment with        GC-enriched mRNA (R2791). The statistical significance was        assessed by the Mann Whitney test (p=0.03).

FIGS. 9A-B: Luciferase activity expressed by wild type or modifiedmRNAs.

-   -   Both RNAs were separately transfected into HeLa cells and        luciferase activity (relative light units, RLU) was measured 6        h, 24 h and 48 h after transfection as described in Example 2.    -   (A) The luciferase activity of GC-enriched mRNA (R875) and        C-optimized mRNA (R2103) was comparable both in terms of peak        level and kinetics indicating a comparable expression level of        the transfected mRNAs as a function of time.    -   (B) The luciferase activity of GC-enriched mRNA (R875) was much        higher than that of the wild type construct (R873) indicating a        significantly increased expression level of the modified G/C        enriched mRNA.

FIG. 10: Dose-response relationship for TNFα secretion of human PBMCstreated with different modified mRNAs.

-   -   Human PBMCs were treated with different concentrations of mRNAs        (40 and 20 μg/ml) for 20 hours. The TNFα concentration as a        parameter indicating the immune response evoked by the        transfected mRNA in the immunologically competent PBMCs was        determined by ELISA in the supernatants as described in        Example 3. Treatment with C-optimized mRNA results in less TNFα        secretion than treatment with GC-optimized mRNA. The mean and        standard error of mean of triplicates are shown.

FIG. 11: Dose-response relationship for IFNαsecretion of human PBMCstreated with various modified mRNAs.

-   -   Human PBMCs were treated with different concentrations of mRNAs        (40 and 20 μg/ml) as indicated for 20 hours. The        IFNαconcentration was determined by ELISA in the supernatants as        described in Example 3. Transfection of the PBMCs with        C-optimized mRNA results in less IFNαsecretion than transfection        with GC-optimized mRNA. The mean and standard error of mean of        triplicates are shown.

Table 1: List of luciferase constructs used for the production of thewild type (R873) and G/C- or C-enriched modified mRNA constructs used.

Table 2: Summary of the nucleotide composition and codon usage of theconstructs used in the present Examples.

DETAILED DESCRIPTION OF THE INVENTION

Although the present invention is described in detail below, it is to beunderstood that this invention is not limited to the particularmethodologies, protocols and reagents described herein as these mayvary. It is also to be understood that the terminology used herein isfor the purpose of describing particular embodiments only, and is notintended to limit the scope of the present invention, which will belimited only by the appended claims. Unless defined otherwise, alltechnical and scientific terms used herein have the same meanings ascommonly understood by one of ordinary skill in the art.

In the following, the elements of the present invention will bedescribed. These elements are listed with specific embodiments, however,it should be understood that they may be combined in any manner and inany number to create additional embodiments. The variously describedexamples and preferred embodiments should not be construed to limit thepresent invention to only the explicitly described embodiments. Thisdescription should be understood to support and encompass embodimentswhich combine the explicitly described embodiments with any number ofthe disclosed and/or preferred elements. Furthermore, any permutationsand combinations of all described elements in this application should beconsidered as disclosed by the description of the present application,unless the context indicates otherwise.

Throughout this specification and the claims which follow, unless thecontext requires otherwise, the term “comprise”, and variations such as“comprises” and “comprising”, will be understood to imply the inclusionof a stated member, integer or step but not the exclusion of any othernon-stated member, integer or step. The term “consist of” is aparticular embodiment of the term “comprise”, wherein any othernon-stated member, integer or step is excluded. In the context of thepresent invention, the term “comprise” encompasses the term “consistof”.

The terms “a” and “an” and “the” and similar reference used in thecontext of describing the invention (especially in the context of theclaims) are to be construed to cover both the singular and the plural,unless otherwise indicated herein or clearly contradicted by context.Recitation of ranges of values herein is merely intended to serve as ashorthand method of referring individually to each separate valuefalling within the range. Unless otherwise indicated herein, eachindividual value is incorporated into the specification as if it wereindividually recited herein. No language in the specification should beconstrued as indicating any non-claimed element essential to thepractice of the invention.

Several documents are cited throughout the text of this specification.Each of the documents cited herein (including all patents, patentapplications, scientific publications, manufacturer's specifications,instructions, etc.), whether supra or infra, are hereby incorporated byreference in their entirety. Nothing herein is to be construed as anadmission that the invention is not entitled to antedate such disclosureby virtue of prior invention.

The present invention is based on the surprising finding that the immuneresponse against a target mRNA, which encodes at least one biologicallyactive polypeptide or protein, can be modulated, i.e. reduced, by theinventive method of increasing the cytosine-content of the coding regionof the mRNA. The inventive method hereby comprises the step ofidentifying a target wild type sequence, which encodes for at least onebiologically active peptide, polypeptide or protein. As a second step,the target wild type sequence is modified, whereby at least 70% of thecodons, or at least 80% of the codons, or more preferably at least 90%,or most preferably 100% of the wild type codons of the coding region,which are cytosine content-optimizable are modified such that theoverall cytosine-content of the region of the modified mRNA coding forthe peptide, polypeptide or protein is increased over thecytosine-content of the coding region of the wild type mRNA coding forthe at least one peptide, polypeptide or protein. By that modification,the amino acid sequence encoded by the modified mRNA is unchangedcompared to the wild type sequence.

Due to the naturally occuring degeneracy of the genetic code, more thanone codon may encode a particular amino acid. Accordingly, 18 out of 20naturally occuring amino acids are encoded by more than 1 codon (withTryp and Met being an exception), e.g. by 2 codons (e.g. Cys, Asp, Glu),by three codons (e.g. Ile), by 4 codons (e.g. Al, Gly, Pro) or by 6codons (e.g. Leu, Arg, Ser). However, not all codons encoding the sameamino acid are utilized equally frequent under in vivo conditions.Depending on each single organism, a typical codon usage profile isestablished.

The term “cytosine content-optimizable codon” as used within the contextof the present invention refers to codons, which exhibit a lower amountof cytosines than other codons coding for the same amino acid.Accordingly, any wild type codon, which may be replaced by another codoncoding for the same amino acid and exhibiting a higher number ofcytosines within that codon, is considered to be cytosine-optimizable(C-optimizable). Any such substitution of a C-optimizable wild typecodon by the specific C-optimized codon within a wild type coding regionincreases its overall C-content and reflects a C-enriched modified mRNAsequence. A C-maximized mRNA sequence contains C-optimized codons forall potentially C-optimizable codons. Accordingly, 100% or all of thetheoretically replaceable C-optimizable codons are under such conditionsactually replaced by C-optimized codons over the entire length of thecoding region.

Within the context of the present invention the preferred cell is amammalian cell, more preferably a human cell. The codon usage frequencyfor the individual codons is provided in Table 2 of the appendedexamples. The term “coding region” as used in the present invention,i.e. the region in which the cytosine-content is increased by the use ofcytosine-content optimized codons, corresponds to that portion of anRNA, such as, e.g. an mRNA, that codes for a peptide, polypeptide orprotein. The coding region in mRNA may be bounded by the five primeuntranslated region (5′ UTR) and the three prime untranslated region (3′UTR).

Within the present invention, cytosine-content optimizable codons arecodons, which contain a lower number of cytosines than other codonscoding for the same amino acid.

Any of the codons GCG, GCA, GCU codes for the amino acid Ala, which maybe exchanged by the codon GCC encoding the same amino acid, and/or

the codon UGU that codes for Cys may be exchanged by the codon UGCencoding the same amino acid, and/or

the codon GAU which codes for Asp may be exchanged by the codon GACencoding the same amino acid, and/or

the codon that UUU that codes for Phe may be exchanged for the codon UUCencoding the same amino acid, and/or

any of the codons GGG, GGA, GGU that code Gly may be exchanged by thecodon GGC encoding the same amino acid, and/or

the codon CAU that codes for His may be exchanged by the codon CACencoding the same amino acid, and/or

any of the codons AUA, AUU that code for Ile may be exchanged by thecodon AUC, and/or any of the codons UUG, UUA, CUG, CUA, CUU coding forLeu may be exchanged by the codon CUC encoding the same amino acid,and/or

the codon AAU that codes for Asn may be exchanged by the codon AACencoding the same amino acid, and/or

any of the codons CCG, CCA, CCU coding for Pro may be exchanged by thecodon CCC encoding the same amino acid, and/or

any of the codons AGG, AGA, CGG, CGA, CGU coding for Arg may beexchanged by the codon CGC encoding the same amino acid, and/or

any of the codons AGU, AGC, UCG, UCA, UCU coding for Ser may beexchanged by the codon UCC encoding the same amino acid, and/or

any of the codons ACG, ACA, ACU coding for Thr may be exchanged by thecodon ACC encoding the same amino acid, and/or

any of the codons GUG, GUA, GUU coding for Val may be exchanged by thecodon GUC encoding the same amino acid, and/or

the codon UAU coding for Tyr may be exchanged by the codon UAC encodingthe same amino acid.

In any of the above instances, the number of cytosines is increased by 1per exchanged codon. Exchange of all non C-optimized codons(corresponding to C-optimizable codons) of the coding region results ina C-maximized coding sequence. According to the invention at least 70%of the non C-optimized codons are replaced by C-optimized codons of thewild type sequence are replaced by C-optimized codons, preferably atleast 80%, more preferably at least 90% within the coding region.

It may be preferred that for some amino acids the percentage ofC-optimizable codons replaced by C-optimized codons is less than 70%,while for other amino acids the percentage of replaced codons is higherthan 70% to meet the overall percentage of C-optimization of at least70% of all C-optimizable wild type codons of the coding region.

Preferably, in the C-optimized mRNAs of the invention, at least 50% ofthe C-optimizable wild type codons for any given amino acid are replacedby C-optimized codons, e.g. any modified C-enriched mRNA preferablycontains at least 50% C-optimized codons at C-optimizable wild typecodon positions coding for any single of the above mentioned amino acidsAla, Cys, Asp, Phe, Gly, His, Ile, Leu, Asn, Pro, Arg, Ser, Thr, Val andTyr, preferably at least 60%.

According to the inventive method, codons coding for amino acids, whichare not cytosine content-optimizable and which are, however, encoded byat least two codons, may be used without any further selection process.However, in a preferred embodiment of the invention the codon of thewild type sequence that codes for a relatively rare tRNA in the cell,e.g. a human cell, is exchanged for a codon that codes for a relativelyfrequent tRNA in the cell, whereby both code for the same amino acid.Accordingly, the relatively rare codon GAA coding for Glu may beexchanged by the relative frequent codon GAG coding for the same aminoacid, and/or

the relatively rare codon AAA coding for Lys may be exchanged by therelative frequent codon AAG coding for the same amino acid, and/or

the relatively rare codon CAA coding for Gln is exchanged for therelative frequent codon CAG encoding the same amino acid.

In accordance with the present invention, the amino acids Met (AUG) andTrp (UGG), which are encoded by only one codon each, remain unchanged.Stop codons are not cytosine-content optimized, however, the relativelyrare stop codons amber, ochre (UAA, UAG) may be exchanged by therelatively frequent stop codon opal (UGA).

The substitutions listed above may obviously be used individually butalso in all possible combinations in order to optimize thecytosine-content of the modified mRNA compared to the wild type mRNAsequence.

Accordingly, the region of the modified mRNA coding for the polypeptideor protein is changed compared to the coding region of the polypeptideor protein of the wild type mRNA in such a way that an amino acidencoded by at least two or more codons, of which one comprises oneadditional cytosine, such a codon may be exchanged by the C-optimizedcodon comprising one additional cytosine, whereby the amino acid isunaltered compared to the wild type sequence.

In a preferred embodiment, the modified mRNA has—in addition to anincreased C-content as defined above—an increased guanosine-content(G-content). In analogy to the modifications described above, whichresult in an increased C-content, corresponding modifications mayadditionally be introduced, which result in a higher G-content of themodified mRNA. Therein, a codon in the mRNA, which is guanosine-contentoptimizable, is replaced by a codon with a higher guanosine-content.Generally, the definitions and explanations provided above with respectto cytosine-optimizable codons and increased C-content apply toguanosine-optimizable codons and G-content in analogous manner. In thecontext of the present invention, guanosine-optimizable codons arecodons, which contain a lower number of guanosines than other codonsthat are encoding the same amino acid.

In a further preferred embodiment, the modified mRNA is modified suchthat at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90%, preferablyat least 70% of the codons, which are not eligible for C-optimization,but which are guanosine-content optimizable, are replaced by a codonwith a higher guanosine content, thus increasing the G-content of themodified mRNA.

Alternatively, the modified mRNA may be obtained by the followingapproach:

As a first step, its G/C content may be increased, e.g. by substitutingwild type codons exhibiting a lower content of G and C nucleotides. Atleast 70%, more preferably at least 80%, more preferred at least 90%, ormost preferred 100% of all wild type codons, which are G/C optimizable,may be replaced by that approach. G/C optimization is carried out asdisclosed in WO2002098443 A2. As a second step, the G/C-enrichment ormaximization is followed by a step of further C-optimization.Accordingly, the G/C optimized codons and/or the unaltered codons withinthe coding region are C-optimized by selecting codons, which exhibit ahigher number of cytsines as compared to the codons occurring in theG/C-enriched mRNA. At least 70%, more preferably at least 80%, morepreferably at least 90%, most preferred 100% of those GC-optimized andunaltered codons, which are C-optimizable, are replaced by that secondstep. The second step coincides with the first step (as described abovefor the embodiment starting with C-enrichment), but starts from a codonpattern, which is different from the wild type codon pattern. As aresult, G/C maximization and subsequent C-maximization over the entirelength of the coding region usually results in the same coding sequenceas the alternative embodiment starting with C-maximization andsubsequent G-maximization as described above.

According to a further embodiment of the present invention, the cytosinecontent of the coding region of the target mRNA coding for thepolypeptide or protein is modified such that a maximal cytosine-contentis achieved by introduction of codons, which code for tRNAs, which arerelatively frequent within that particular cell, e.g. such as amammalian cell, more specifically a human cell.

According to the inventive method for targeted modulation, preferablyreduction, of the immune response against an mRNA, the cytosine contentof the modified mRNA, which encodes at least one biologically activepolypeptide or protein, is increased by at least 1-15%, preferably5-10%, preferably by at least 10-15%, preferably by at least 10%, morepreferably by at least 12.5%, more specifically by at least 15% comparedto the cytosine content of the wild type sequence.

According to the present invention, it is thus particularly preferred toincrease the cytosine content of the modified mRNA by the maximum amountpossible, in particular in the coding region for the at least onepeptide or polypeptide, compared to the wild type sequence.

Preferably, the nucleosides, which are introduced into the modified mRNAin order to increase the G and/or C content, are selected from the groupconsisting of adenosine, cytosine, guanosine and uridine. Preferably,the modified RNA is modified only with respect to its G and/or C contentas described herein, wherein (non-modified) cytosine or guanosinereplaces other nucleosides in order to increase the G and/or C contentas described herein. Thus, no analogs of the nucleosides adenosine,cytosine, guanosine and uridine, preferably no nucleoside orribonucleoside analogs as defined herein, are preferably used.

Preferably, the modified mRNA is not modified with a chemicalmodification at the 4-, 5- or 6-position of the pyrimidine base of thenucleosides of cytidine and/or uridine; a chemical modification at the2-, 6-, 7- or 8-position of the purine base of the nucleosides ofadenosine, inosine and/or guanosine; and/or a chemical modification atthe 2′-position of the sugar of the nucleosides of adenosine, inosine,guanosine, cytidine and/or uridine.

More preferably, the modified mRNA is not modified with a chemicalmodification at the 2-, 6-, 7- or 8-position of the purine base of thenucleosides of adenosine, inosine and/or guanosine; and a chemicalmodification at the 2′-position of the sugar of the nucleosides ofadenosine, inosine, guanosine, cytidine and/or uridine.

Even more preferably, the modified mRNA is not modified with a chemicalmodification at the 4-, 5-or 6-position of the pyrimidine base of thenucleosides of cytidine and/or uridine; and a chemical modification atthe 2′-position of the sugar of the nucleosides of adenosine, inosine,guanosine, cytidine and/or uridine.

Preferably, the modified mRNA is not modified with a chemicalmodification at the 5- or 6-position of the pyrimidine base of thenucleosides cytidine and/or uridine, wherein the chemical modificationis preferably selected from the group consisting of 4-thio,5-iodo-/(5-I—), 5-bromo-/(5-Br—), 5-aminoallyl-, 5-fluoro-/(5-F—),5-hydroxy-, 5-hydro-/(5-H—), 5-nitro-, 5-propynyl-/(5-(C

C—CH3)-), 5-methyl-, 5-methyl-2-thio-, 5-formyl-, 5-hydroxymethyl-,5-methoxy-, 5-oxyacetic acid methyl ester-, 5-oxyacetic acid-,5-carboxyhydroxymethyl-, 5-(carboxyhydroxymethyl)pyrimidine methylester-, 5-methoxycarbonylmethyl-, 5-methoxycarbonylmethyl-2-thio,5-aminomethyl-, 5-aminomethyl-2-thio-, 5-aminomethyl-2-seleno-,5-methylaminomethyl-, 5-carbamoylmethyl-, 5-carboxymethylaminomethyl-,5-carboxymethylaminomethyl-2-thio-, 5-carboxymethyl-, 5-methyldihydro-,5-taurinomethyl-, 5-taurinomethyl-2-thiouridine,5-isopentenylaminomethyl-, 5-isopentenylaminomethyl-2-thio-,5-aminopropyl-/(5-(C3H6NH3)-),5-methoxy-ethoxy-methyl-/(5-(CH2-O-C2H4-O-CH3)-) and G-aza-.

Further, the modified mRNA is not modified with a chemical modificationat the 2-, 6-, 7- or 8-position of the purine base of the nucleosidesadenosine, inosine and/or guanosine, wherein the chemical modificationis preferably selected from the group consisting of 2-Amino-, 7-Deaza-,8-Aza- and 8-Azido-.

In addition or alternatively, the modified mRNA is not modified with achemical modification at the 2′-position of the sugar of the nucleosidesadenosine, inosine, guanosine, cytidine and/or uridine, whenincorporated in the RNA sequence, wherein such chemical modifications atthe 2′-position of the sugar of the nucleosides adenosine, inosine,guanosine, cytidine and/or uridine may be selected from the groupconsisting of 2′-deoxy-, 2′-amino-2′-deoxy-/2′-amino-,2′-fluoro-2′-deoxy-/2′-fluoro- and 2′-O-methyl-2′-deoxy-/2′-O-methyl-.

Preferably, the modified mRNA is not modified with a chemicalmodification at the 4,-5- or 6-position of the base pyrimidine of thenucleosides cytidine and/or uridine and at the 2′-position of the ribosesugar as defined above, wherein the chemical modification is preferablyselected from the group consisting of 4-thio-2′-deoxy-,4-thio-2′-amino-, 4-thio-2′-fluoro-, 4-thio-2′-O-methyl-,5-iodo-2′-deoxy-, 5-iodo-2′-amino-, 5-iodo-2′-fluoro-,5-iodo-2′-O-methyl-, 5-bromo-2′-deoxy-, 5-bromo-2′-amino-,5-bromo-2′-fluoro-, 5-bromo-2′-O-methyl-, 5-aminoallyl-2′-deoxy-,5-aminoallyl-2′-amino-, 5-aminoallyl-2′-fluoro-,5-aminoallyl-2′-O-methyl-, 5-fluoro-2′-deoxy-, 5-fluoro-2′-amino-,5-fluoro-2′-fluoro-, 5-fluoro-2′-O-methyl-, 5-hydroxy-2′-deoxy-,5-hydroxy-2′-amino-, 5-hydroxy-2′-fluoro-, 5-hydroxy-2′-O-methyl-,5-hydro-2′-deoxy-, 5-hydro-2′-amino-, 5-hydro-2′-fluoro-,5-hydro-2′-O-methyl-, 5-nitro-2′-deoxy-, 5-nitro-2′-amino-,5-nitro-2′-fluoro-, 5-nitro-2′-O-methyl-, 5-propynyl-2′-deoxy-,5-propynyl-2′-amino-, 5-propynyl-2′-fluoro-, 5-propynyl-2′-O-methyl-,5-methyl-2′-deoxy-, 5-methyl-2′-amino-, 5-methyl-2′-fluoro-,5-methyl-2′-O-methyl (5,2′-O-dimethyl)-, 5-methyl-2-thio-2′-deoxy-,5-methyl-2-thio-2′-amino-, 5-methyl-2-thio-2′-fluoro-,5-methyl-2-thio-2′-O-methyl-, 5-formyl-2′-deoxy-, 5-formyl-2′-amino-,5-formyl-2′-fluoro-, 5-formyl-2′-O-methyl-, 5-hydroxymethyl-2′-deoxy-,5-hydroxymethyl-2′-amino-, 5-hydroxymethyl-2′-fluoro-,5-hydroxymethyl-2′-O-methyl-, 5-methoxy-2′-deoxy-, 5-methoxy-2′-amino-,5-methoxy-2′-fluoro-, 5-methoxy-2′-O-methyl-, 5-oxyacetic acid methylester-2′-deoxy-, 5-oxyacetic acid methyl ester-2′-amino-, 5-oxyaceticacid methyl ester-2′-fluoro-, 5-oxyacetic acid methylester-2′-O-methyl-, 5-oxyacetic acid-2′-deoxy-, 5-oxyaceticacid-2′-amino-, 5-oxyacetic acid-2′-fluoro-, 5-oxyaceticacid-2′-O-methyl-, 5-carboxyhydroxymethyl-2′-deoxy-,5-carboxyhydroxymethyl-2′-amino-, 5-carboxyhydroxymethyl-2′-fluoro-,5-carboxyhydroxymethyl-2′-O-methyl-, 5-(carboxyhydroxymethyl)pyrimidinemethyl ester-2′-deoxy-, 5-(carboxyhydroxymethyl)pyrimidine methylester-2′-amino-, 5-(carboxyhydroxymethyl)pyrimidine methylester-2′-fluoro-, 5-(carboxyhydroxymethyl)pyrimidine methylester-2′-O-methyl-, 5-methoxycarbonylmethyl-2′-deoxy-,5-methoxycarbonylmethyl-2′-amino-, 5-methoxycarbonylmethyl-2′-fluoro-,5-methoxycarbonylmethyl-2′-O-methyl-, 5-methoxycarbonylmethyl-2-thio2′-deoxy-, 5-methoxycarbonylmethyl-2-thio 2′-amino-,5-methoxycarbonylmethyl-2-thio 2′-fluoro-,5-methoxycarbonylmethyl-2-thio 2′-O-methyl-, 5-aminomethyl-2′-deoxy-,5-aminomethyl-2′-amino-, 5-aminomethyl-2′-fluoro-,5-aminomethyl-2′-O-methyl-, 5-aminomethyl-2-thio-2′-deoxy-,5-aminomethyl-2-thio-2′-amino-, 5-aminomethyl-2-thio-2′-fluoro-,5-aminomethyl-2-thio-2′-O-methyl-, 5-aminomethyl-2-seleno-2′-deoxy-,5-aminomethyl-2-seleno-2′-amino-, 5-aminomethyl-2-seleno-2′-fluoro-,5-aminomethyl-2-seleno-2′-O-methyl-, 5-methylaminomethyl-2′-deoxy-,5-methylaminomethyl-2′-amino-, 5-methylaminomethyl-2′-fluoro-,5-methylaminomethyl-2′-O-methyl-, 5-carbamoylmethyl-2′-deoxy-,5-carbamoylmethyl-2′-amino-, 5-carbamoylmethyl-2′-fluoro-,5-carbamoylmethyl-2′-O-methyl-, 5-carboxymethylaminomethyl-2′-deoxy-,5-carboxymethylaminomethyl-2′-amino-,5-carboxymethylaminomethyl-2′-fluoro-,5-carboxymethylaminomethyl-2′-O-methyl-,5-carboxymethylaminomethyl-2-thio-2′-deoxy-,5-carboxymethylaminomethyl-2-thio-2′-amino-,5-carboxymethylaminomethyl-2-thio-2′-fluoro-,5-carboxymethylaminomethyl-2-thio-2′-O-methyl-,5-carboxymethyl-2′-deoxy-, 5-carboxymethyl-2′-amino-,5-carboxymethyl-2′-fluoro-, 5-carboxymethyl-2′-O-methyl-,5-methyldihydro-2′-deoxy-, 5-methyldihydro-2′-amino-,5-methyldihydro-2′-fluoro-, 5-methyldihydro-2′-O-methyl-,5-taurinomethyl-2′-deoxy-, 5-taurinomethyl-2′-amino-,5-taurinomethyl-2′-fluoro-, 5-taurinomethyl-2′-O-methyl-,5-taurinomethyl-2-thiouridine-2′-deoxy-,5-taurinomethyl-2-thiouridine-2′-amino-,5-taurinomethyl-2-thiouridine-2′-fluoro-,5-taurinomethyl-2-thiouridine-2′-O-methyl-,5-isopentenylaminomethyl-2′-deoxy-, 5-isopentenylaminomethyl-2′-amino-,5-isopentenylaminomethyl-2′-fluoro-,5-isopentenylaminomethyl-2′-O-methyl-,5-isopentenylaminomethyl-2-thio-2′-deoxy-,5-isopentenylaminomethyl-2-thio-2′-amino-,5-isopentenylaminomethyl-2-thio-2′-fluoro-,5-isopentenylaminomethyl-2-thio-2′-O-methyl-, 5-aminopropyl-2′-deoxy-,5-aminopropyl-2′-amino-, 5-aminopropyl-2′-fluoro-,5-aminopropyl-2′-O-methyl-, 5-methoxy-ethoxy-methyl-2′-deoxy-,5-methoxy-ethoxy-methyl-2′-amino-, 5-methoxy-ethoxy-methyl-2′-fluoro-,5-methoxy-ethoxy-methyl-2′-O-methyl-, 6-aza-2′-deoxy-, 6-aza-2′-amino-,6-aza-2′-fluoro- and 6-aza-2′-O-methyl-.

More preferably, the modified mRNA is not modified with a chemicalmodification at the 2-, 6-, 7- or 8-position of the purine base of thenucleosides adenosine, inosine and/or guanosine and at the 2′-positionof the ribose sugar as defined above, wherein the chemical modificationis selected from the group consisting of 2-Amino-2′-deoxy-,2-Amino-2′-amino-, 2-Amino-2′-fluoro-, 2-Amino-2′-O-methyl-,7-Deaza-2′-deoxy-, 7-Deaza-2′-amino-, 7-Deaza-2′-fluoro-,7-Deaza-2′-O-methyl-, 8-Aza-2′-deoxy-, 8-Aza-2′-amino-,8-Aza-2′-fluoro-, 8-Aza-2′-O-methyl-, 8-Azido-2′-deoxy-,8-Azido-2′-amino-, 8-Azido-2′-fluoro- and 8-Azido-2′-O-methyl-.

According to the invention, the term polypeptide or protein refers to apeptide having at least 20, and preferably more than 50 amino acids. Itmay refer to a monomeric or multimeric protein. A peptide is understoodto contain typically less than 20 amino acids.

According to the first embodiment of the present invention, the term“biologically active peptide, polypeptide or protein” refers to apolypeptide or protein that has the capability of performing one or morebiological functions or a set of activities normally attributed to thepolypeptide in a biological context. The biological activity may e.g. bea receptor binding activity, e.g. as a ligand, a catalytic activity, atransporter activity or an activity induced in cell structure proteinsor modifications of cellular proteins, such as e.g. phosphorylation. Thebiological activity of the peptide, polypeptide or protein encoded bythe wild type or by the modified mRNA according to the invention can bedetermined by any method available in the art. For example, thebiological activity of members of the interferon family of proteins canbe determined by any of a number of methods including their interactionwith interferon-specific antibodies, their ability to increaseresistance to viral infection, or their ability to modulate thetranscription of interferon-regulated gene targets.

In a preferred embodiment, the biologically active peptide, polypeptideor protein does not comprise the gene product of a reporter gene or amarker gene. In the context of the present invention, the mRNA doespreferably not encode, for instance, luciferase; green fluorescentprotein (GFP) and its variants (such as eGFP, RFP or BFP); α-globin;hypoxanthine-guanine phosphoribosyltransferase (HGPRT); β-galactosidase;galactokinase; alkaline phosphatase; secreted embryonic alkalinephosphatase (SEAP)) or a resistance gene (such as a resistance geneagainst neomycin, puromycin, hygromycin and zeocin). In a preferredembodiment, the mRNA does not encode luciferase. In another embodiment,the mRNA does not encode GFP or a variant thereof.

In a further preferred embodiment, the biologically active peptide,polypeptide or protein does not comprise a protein (or a fragment of aprotein) derived from a virus, preferably from a virus belonging to thefamily of Orthomyxoviridae. Preferably, the mRNA does not encode aprotein that is derived from an influenza virus, more preferably aninfluenza A virus. Preferably, the mRNA does not encode an influenza Aprotein selected from the group consisting of hemagglutinin (HA),neuraminidase (NA), nucleoprotein (NP), matrix protein M1, matrixprotein M2, NS1, NS2 (NEP: nuclear export protein), PA, PB1 (polymerasebasic 1), PB1-F2 and PB2. In another preferred embodiment, the mRNA doesnot encode ovalbumin (OVA) or a fragment thereof. Preferably, the mRNAdoes not encode an influenza A protein or ovalbumin.

By the method according to the invention, an optimum balance ofincreased mRNA stability on the one hand and reduced immunostimulatoryproperties on the other hand is achieved. Increased C-content of themodified mRNA reduces the mRNA's immunogenicity and/or immunostimulatorycapacity, while the increased C and G content contribute to increasedmRNA stability. Increased mRNA stability means, e.g. increased in vivofunctional stability resulting in an increased level of expressedprotein over time. Accordingly, the in vivo AUC (area under the curve)of detectable protein upon mRNA administration is significantlyincreased for the inventive modified mRNA as compared to its wild typeequivalent. Simultaneously, a reduced immune response in the patient isevoked (as determinable, for instance, by reduced amounts of cytokinessecreted upon mRNA administration). The level of cytokine expression(secretion), e.g. TNF-α and IFN-α (e.g. by PBMCs) is reduced by at least20%, preferably by at least 40%, as compared to the immune responsetriggered by the wild type equivalent. Such a reduction is measurableunder in vivo and in vitro conditions.

According to the method of the present invention, the codon adaptationindex of the modified target mRNA encoding at least one biologicallyactive polypeptide or protein is increased by at least 0.05-0.5, or byat least 0.1-0.4, or by at least 0.2-0.3, or by at least 0.075-0.2, orby at least 0.1-0.2, or by at least 0.05, or by at least 0.1, or by atleast 0.2, preferably by at least 0.125, more preferably by at least0.15 compared to the CAI of the wild type mRNA.

The Codon Adaptation Index (CAI) is the most widespread technique foranalyzing codon usage bias. The CAI provides an indication of geneexpression level under the assumption that there is translationalselection to optimize gene sequences according to their expressionlevels.

The codon adaptation index as used in the present invention can becalculated according to the method as published by Sharp and Li (NucleicAcids Res. 1987 Feb. 11; 15(3):1281-95). Software-implemented solutionsfor the calculation of the CAI are also known in prior art, such as e.g.“The CAI Analyser Package” (Ramazotti et al, In Silico Biol. 2007;7(4-5):507-26) and are thus readily available to the skilled person. CAIis simply defined as the geometric mean of the weight associated to eachcodon over the length of the gene sequence (measured in codons). Foreach amino acid, the weight of each of its codons, in CAI, is computedas the ratio between the observed frequency of the codon and thefrequency of the synonymous codon for that amino acid. The CAI uses areference set of highly expressed genes from a species to determinerelative merit of each codon to calculate a score for a gene from thefrequency of use of all codons in said gene. This index is useful forpredicting the level of expression of a gene and indicate likely successof heterologous gene expression in a given cell system.

Within the scope of the present invention, the term codon adaptationindex (CAI) as used herein relates to the codon usage frequency of thegenes encoding the at least one polypeptide or protein. Codon adaptationis the adaptation of the codons of an open reading frame to thesynonymous codons preferred in human/mammalian genes whilst avoiding theintroduction of unwanted secondary sequence functions that impedeexpression of the resulting open reading frames.

Within the context of the present invention, a CAI score of 1 means thatthe optimal codon is used for each amino acid in each codon position.Thus, according to the methods of the present invention, the codingregion of the mRNA has a CAI which is greater than the CAI of thecorresponding wild coding type sequence and the CAI of the modified mRNAis sufficiently close to 1, at least 0.6, more preferably at least 0.7,more preferably at least 0.8 and more preferably at least 0.9, such thatthe desired level of expression of the at least one biologically activepolypeptide or protein is achieved. Accordingly the CAI of the modifiedmRNA is at least greater by 0.05-0.5, or at least greater by 0.1-0.4, orat least greater by 0.2-0.3, or at least greater by 0.075-0.2, or atleast greater by 0.1-0.2, or at least greater by 0.05, or at leastgreater by 0.1, or at least greater by 0.2, preferably at least greaterby 0.125, more preferably at least greater by 0.15, than the CAI of thewild type mRNA region coding for the at least one biologically activepolypeptide or protein.

According to a preferred embodiment, the present invention provides amodified mRNA encoding at least one biologically active polypeptide orprotein, which is obtainable or obtained by at least one or moreembodiments of the inventive method of the present invention and whereinthe modified mRNA is characterized by a reduced immunogenicity and/orimmunostimulatory capacity compared to the wild type mRNA and may alsobe characterized by enhanced stability, in particular enhancedfunctional stability, as compared to the wild type equivalent.

In a more preferred embodiment of the present invention, the obtainablemRNA may further be subject to a step of determining the immunogenicityand/or immunostimulatory capacity of the inventive modified mRNA. Such astep comprises the e.g. in vitro sub-steps of transfecting competentcells, e.g. PBMCs, with the modified mRNA according to one or moreembodiments of the inventive method, cultivating the cells, e.g. for8h-24 h, preferably for 12 h -48 h, preferably for 18h-24 h, preferablyfor 24-48 h, preferably for at least 12 hours, preferably for at least18 h, more preferably for at least 20 h and determining the amount ofpro-inflammatory cytokines in the cell supernatant. The amount ofpro-inflammatory cytokines present in the supernatant of the cellstransfected with the modified mRNA according to the invention iscompared to the amount of pro-inflammatory cytokines present in thesupernatant of cells transfected with the wild type mRNA equivalent.

Appropriate techniques for determining the immunogenicity and/orimmunostimulatory capacity of a nucleic acid, such as that of e.g. theinventive modified mRNA, are known in the art and are readily availableto the skilled person (Robbins et al., 2009. Oligonucleotides19(2):89-102). The nature and the extent of the cytokine response to RNAdepends on several factors including timing, cell type, delivery vehicleand route of administration. The absence of immunostimulation at asingle time point for a single cytokine does not necessarily demonstratethe absence of immunostimulation in general, such that assessment ofseveral cytokine responses at multiple time points may be required.Antibodies and ELISA kits for the determination of interferons (e.g.IFNα and IFNβ) and a variety of pro-inflammatory cytokines, such as e.g.TNFα, TGFP, IL-1 and IL-6, are commercially available.

If it were desired to carry out in vivo studies for testing for IFNαand/or suitable pro-inflammatory cytokines, such as e.g. TNFα and IL-6,their presence in the plasma of treated animals can be used to monitorthe systemic activation of the immune response. Measurement of theimmune response at an appropriate time point after mRNA administrationis critical for a valid assessment. Systemic administration of mRNAformulations to mice leads to detectable elevations of serum cytokineswithin 1 to 2 hours, depending on the type of delivery vehicle and thecytokine of interest. Typically, the increase of cytokine levels in theserum is transient and may decrease again after 12 to 24 hours oftreatment. For example, mice can be injected with complexed mRNA andserum levels of, e.g., IFNα, TNFα and IL-6 may be measured 6 hours postinjection by using suitable ELISA assays (Kariko et al., 2012. Mol.Ther. 20(5):948-53).

For in vitro studies, a similar panel of cytokines can be used to assessthe stimulation of primary immune cell cultures after treatment withmRNA of the invention. The secretion of cytokines is cell type-dependentand therefore several cytokines may be required to be tested. Theassessment of cytokine responses from in vitro cell cultures is lesstime critical compared to in vivo studies because the secreted cytokinestend to accumulate in the cell culture supernatant. Therefore, themeasurement of cytokines at a single time point, such as between 8 h-24h, or between 16-24 h, or between 12 h -48 h, or between 18 h-24 h, orbetween 24-48 h, preferably 12 hours, preferably 18 h, more preferably20 h, after mRNA administration, such as e.g. the treatment with themodified mRNA according to the present invention is often sufficient todetect an immune response. For example, a human in vitro whole bloodassay (WBA) or peripheral blood mononuclear cell (PBMC) based assay canbe used to assess the cytokine response elicited by treatment withmodified mRNA molecules of the invention (Coch et al., 2013. PLoS One8(8):e71057), as exemplified in the appended examples, in particularExample 2. Alternatively, primary myeloid and plasmacytoid dendriticcells (pDCs) can be isolated from peripheral blood using commerciallyavailable cell isolation kits and are treated with mRNA of theinvention, such as the modified mRNA according to the invention, in cellculture. After 8 to 20 hours of incubation cytokine levels (e.g. IFNα,TNFα and/or IL-8) in the cell culture medium may be determined withELISA assays. In addition, the activation status of DCs may be analyzedby measuring cell surface expression of activation markers (e.g. CD80,CD83, CD86 and MHC class II) by flow cytometry (Kariko et al., 2005.Immunity 23(2):165-75).

Alternatively, activation of the cytosolic RNA sensor RIG-I in cells canbe assessed by treating cells with modified mRNA of the invention,generating cell lysates, separating proteins by SDS-polyacrylamide gelelectrophoresis and probing for phosphorylation of PKR by Westernblotting. Phosphorylation of PKR on threonine at position 446 (pT446) isrequired for PKR activation and thus represents an activation marker. Inaddition, the phosphorylation of the alpha subunit of eukaryotic proteinsynthesis initiation factor-2 (EIF2-alpha), which is a physiologicalsubstrate for PKR, can be assessed with an antibody directed atphosphorylated serine at position 51 (pS51) (Anderson et al., 2010.Nucleic Acids Res. 38(17):5884-92).

The activation of 2′-5′ oligoadenylate synthetase (OAS) by RNA can betested in an enzyme assay. The assay for OAS can be performed by themeasurement of the 2-5(A) products. Using [³H]ATP in the synthetasereaction, the conversion of 2-5(A) is measured by digestion of thereaction products with alkaline phosphatase. This converts [³H]2-5(A) tocore (A2′p)_(n)A, which is negatively charged and binds toDEAE-cellulose paper. Residual [³H]ATP is converted to adenosine whichis uncharged and removed by washing. This assay is suitable to measureOAS activity in crude cell extracts as well as that of purified OAS(Sharp et al., 1999. Virology 257(2):303-13; Anderson et al., 2011.Nucleic Acids Res. 39(21):9329-38).

Typically, the inventive modified mRNA obtainable according to one ormore embodiments of the inventive method for targeted modulation of theimmune response against an mRNA is characterized by lower affinity toone or more of TLR3, TLR7, TLR8, MDAS, RIG-I, LGP2 or2′-5′-oligoadenylate synthetase compared to the wild type mRNA encodingthe same peptide, polypeptide or protein.

The term “affinity” as used herein relates to the ability of an RNA,such as e.g. the modified mRNA of the invention, to bind to and/or tofunction as a ligand and/or activate signaling events by one or more ofTLR3, TLR7, TLR8, MDA5, RIG-I, LGP2 or 2′-5′-oligoadenylate synthetase.Thus, RNA, such as the modified mRNA of the present invention, which ischaracterized by lower affinity to one or more of TLR3, TLR7, TLR8,MDA5, RIG-I, LGP2 or 2′-5′-oligoadenylate synthetase will result in areduced production of pro-inflammatory cytokines, such as, e.g. TNFα,TGFβ, IL-1 or IL-6. The affinity may be reduced by at least 50%,preferably by at least 60%, as compared to the affinity of the wild typeequivalent.

Thus, the affinity of the modified mRNA of the present invention to oneor more of TLR3, TLR7, TLR8, MDA5, RIG-I, LGP2 or 2′-5′-oligoadenylatesynthetase is correlated with the amount of pro-inflammatory cytokinesproduced in any one of the above assays, i.e. a reduced affinity and/oractivation of one or more of TLR3, TLR7, TLR8, MDA5, RIG-I, LGP2 or2′-5′-oligoadenylate synthetase is correlated with a reduced amount ofpro-inflammatory cytokines released into the cell supernatant comparedto the amount of pro-inflammatory cytokines, such as, e.g. TNFα, TGFβ,IL-1 or IL-6, produced in response to transfection of corresponding wildtype mRNA encoding the at least one biologically active polypeptide orprotein.

In a preferred embodiment, the inventive method of targeted modulationof the immune response against an mRNA encoding at least onebiologically active polypeptide or protein according to the presentinvention may be executed on a computer with the aid of suitablesoftware by way of executing at least one algorithm thereon.

Computer software for sequence analysis and/or codon optimization isknown in prior art and is readily accessible to the skilled person.Computer programs, which may be used to execute the at least onealgorithm of the inventive method may include, e.g. CodonW, GCUA, INCA,etc. Also, several software packages that are available online may beused, such as e.g. the “JCat” available on the world wide web atjcat.de/. The at least one algorithm may, e.g. comprise the followingsteps:

-   -   1. Providing the wild type target mRNA sequence, such as e.g.        the entire mRNA or a portion thereof. Go to step 2.    -   2. Generate a novel modified mRNA sequence by modifying the        target sequence according to the method as provided in any one        of claims 1-11. Go to step 3.    -   3. Evaluate the modified mRNA sequence and determine if it has a        predetermined property, e.g. at least 70% of the codons of the        wild type mRNA sequence, which are cytosine content optimizable,        have been modified to the maximum C-content possible without        altering the amino acid sequence compared to the wild type        sequence. If the modified mRNA sequence has the predetermined        property, then proceed to step 4, otherwise proceed to step 2.    -   4. Providing the modified mRNA sequence as an optimized and        modified mRNA.

The modified mRNA sequence obtained by the above algorithm may then beused as a template for e.g. chemical RNA synthesis or in vitrotranscription.

According to a further embodiment the inventive modified mRNA coding forat least one biologically active peptide, polypeptide or protein may beobtained by synthesis, such as e.g. chemical synthesis.

Defined chemical synthesis of the modified mRNA of the invention in the3′->5′ direction is well established in prior art. The technologyutilizes a ribonucleoside with suitable N-protecting group: generally5T-Protecting group, the most popular being dimethoxytriphenyl, i.e. theDMT group; T-protecting group, out of which most popular ist-Butyldimethylsilyl ether; and, a 3′-phosphoramidite, the most popularof which is cyanoethyl diisopropyl (component 1). This component is thencoupled with a nucleoside with a suitable N-protecting group, 2′ or 3′succinate of a ribonucleoside attached to a solid support (component 2).The coupling of component 1 and 5′-OH-n-protected-2′,3′-protected-nucleoside (component 3) are also achieved in solutionphase in presence of an activator leading to dimers andoligoribonucleotides, followed by oxidation (3′->5′ directionsynthesis), also leads to a protected dinucleotide having a3′-5′-internucleotide linkage (Ogilvie, K. K., Can. J. Chem., 58, 2686,1980). Other technologies for chemical RNA synthesis, i.e. for thesynthesis of the modified RNA according to the invention are known inprior art, such as, e.g. the method disclosed in US 20110275793 A1.

According to a more preferred embodiment, the modified mRNA according tothe inventive method of the present invention may be obtained by invitro transcription, preferably by bacteriophage-mediated in vitrotranscription, preferably by Sp6 polymerase in vitro transcriptionand/or T3 polymerase-mediated in vitro transcription, more preferably byT7 polymerase-mediated in vitro transcription.

Highly efficient in vitro transcription systems have been developed inprior art, particularly ones using phage polymerases such as T7, SP6,and T3. The DNA-dependent phage T7, T3, and SP6 RNA polymerases arewidely used to synthesize a large quantity of RNAs. These enzymes arehighly processive and are thus capable of generating long RNA moleculesof up to thousands of nucleotides in length with low probability offalling off DNA templates during transcription and may thus be used forin vitro transcription in the present invention. Phage RNA polymerasesspecifically recognize their 18-bp promoter sequences (T7,5′-TAATACGACTCACTATAG (SEQ ID NO: 8); T3, 5′-AATTAACCCTCACTAAAG (SEQ IDNO: 9); and SP6, 5′-ATTTAGGTGACACTATAG (SEQ ID NO: 10)) and initiatetranscription precisely at the 18th nucleotide guanosine. With a T7, T3,or SP6 promoter fused to the 5′ end of a DNA template, the transcriptionreaction is expected to generate an RNA molecule with the predictedsequence.

In this method, a DNA molecule corresponding to the modified mRNA of thepresent invention is transcribed in vitro for the production of themRNA. This DNA matrix has a suitable promoter, for example a T7 and/orSP6 and/or T3 promoter, for the in vitro transcription, followed by thedesired nucleotide sequence for the mRNA to be produced and atermination signal for the in vitro transcription. According to theinvention the DNA molecule that forms the matrix of the RNA construct tobe produced, such as e.g. the modified mRNA according to the presentinvention is prepared by fermentative replication and subsequentisolation as part of a plasmid replicable in bacteria.

Suitable plasmids for in vitro transcription of the modified mRNAaccording to the present invention are known in the art and arecommercially available. For example the following plasmids may bementioned as examples pT7Ts (GeneBank Accession No. U26404), the pGEM®series, for example pGEM®-1 (GeneBank Accession No. X65300) and pSP64(GeneBank-Accession No. X65327); see also Mezei and Storts, Purificationof PCR Products, in: Griffin and Griffin (Eds.), PCR Technology: CurrentInnovation, CRC Press, Boca Raton, Fla., 2001. The in vitrotranscription of the modified mRNA according to the present inventionmay also include ribonucleoside triphosphates (rNTPs) analogues, such asthose, e.g. required for 5′ capping of the in vitro transcribed modifiedmRNA according to the invention. rNTP analogues other than thosenaturally present in mRNAs, in particular mammalian mRNAs, such as e.g.human mRNAs, should not be used for in vitro transcription, since themRNA of the inventive mRNA may be disadvantageously affected and, moreimportantly, if the in vitro transcribed inventive mRNA is to be used inprotein replacement therapy, this may not be in accordance with nationalregulatory affairs.

According to a more preferred embodiment, the modified mRNA that isobtainable by the method according to the present invention may besynthesized by in vitro transcription including naturally occurring rNTPanalogues, for example 5-methyl-cytidine triphosphate and/orpseudouridine triphosphate.

According to a further preferred embodiment, the modified mRNAobtainable by the inventive method may be synthesized by in vitrotranscription, including other than naturally occurring rNTP analogues.

The term “ribonucleoside triphosphate analogues” as used herein refersto ribonucleoside triphosphate compounds comprising a chemicalmodification, wherein the chemical modification may comprise a backbonemodification, a sugar modification, or a base modification. Theseribonucleoside triphosphate analogues are also termed herein as modifiednucleoside triphosphates, modified ribonucleosides or modifiednucleosides.

In this context, the modified nucleoside triphosphates as defined hereinare nucleotide analogs/modifications, e.g. backbone modifications, sugarmodifications or base modifications. A backbone modification in thecontext of the present invention is a modification, in which phosphatesof the backbone of the nucleotides are chemically modified. A sugarmodification in the context of the present invention is a chemicalmodification of the sugar of the nucleotides. Furthermore, a basemodification in in the context of the present invention is a chemicalmodification of the base moiety of the nucleotides. In this contextnucleotide analogs or modifications are preferably selected fromnucleotide analogs, which are applicable for transcription and/ortranslation.

Sugar Modifications

The modified nucleosides and nucleotides, which may be used in thecontext of the present invention, can be modified in the sugar moiety.For example, the 2′ hydroxyl group (OH) can be modified or replaced witha number of different “oxy” or “deoxy” substituents. Examples of “oxy”−2′ hydroxyl group modifications include, but are not limited to, alkoxyor aryloxy (—OR, e.g., R═H, alkyl, cycloalkyl, aryl, aralkyl, heteroarylor sugar); polyethyleneglycols (PEG), —O(CH2CH2o)nCH2CH2OR; “locked”nucleic acids (LNA) in which the 2′ hydroxyl is connected, e.g., by amethylene bridge, to the 4′ carbon of the same ribose sugar; and aminogroups (—O-amino, wherein the amino group, e.g., NRR, can be alkylamino,dialkylamino, heterocyclyl, arylamino, diarylamino, heteroarylamino, ordiheteroaryl amino, ethylene diamine, polyamino) or aminoalkoxy.

“Deoxy” modifications include hydrogen, amino (e.g. NH2; alkylamino,dialkylamino, heterocyclyl, arylamino, diary) amino, heteroaryl amino,diheteroaryl amino, or amino acid); or the amino group can be attachedto the sugar through a linker, wherein the linker comprises one or moreof the atoms C, N, and O.

The sugar group can also contain one or more carbons that possess theopposite stereochemical configuration with respect to that of thecorresponding carbon in ribose. Thus, a modified nucleotide can includenucleotides containing, for instance, arabinose as the sugar.

Backbone Modifications

The phosphate backbone may further be modified in the modifiednucleosides and nucleotides. The phosphate groups of the backbone can bemodified by replacing one or more of the oxygen atoms with a differentsubstituent. Further, the modified nucleosides and nucleotides caninclude the full replacement of an unmodified phosphate moiety with amodified phosphate as described herein. Examples of modified phosphategroups include, but are not limited to, phosphorothioate,phosphoroselenates, borano phosphates, borano phosphate esters, hydrogenphosphonates, phosphoroamidates, alkyl or aryl phosphonates andphosphotriesters. Phosphorodithioates have both non-linking oxygensreplaced by sulfur. The phosphate linker can also be modified by thereplacement of a linking oxygen with nitrogen (bridgedphosphoroamidates), sulfur (bridged phosphorothioates) and carbon(bridged methylene-phosphonates).

Base Modifications

The modified nucleosides and nucleotides, which may be used in thepresent invention, can further be modified in the nucleobase moiety.Examples of nucleobases found in RNA include, but are not limited to,adenine, guanine, cytosine and uracil. For example, the nucleosides andnucleotides described herein can be chemically modified on the majorgroove face. In some embodiments, the major groove chemicalmodifications can include an amino group, a thiol group, an alkyl group,or a halo group.

In particularly preferred embodiments of the present invention, thenucleotide analogs/modifications are selected from base modifications,which are preferably selected from2-amino-6-chloropurineriboside-5′-triphosphate,2-Aminopurine-riboside-5′-triphosphate;2-aminoadenosine-5′-triphosphate,2′-Amino-2′-deoxycytidine-triphosphate, 2-thiocytidine-5′-triphosphate,2-thiouridine-5′-triphosphate, 2′-Fluorothymidine-5′-triphosphate,2T-O-Methyl inosine-5′-triphosphate 4-thiouridine-5′-triphosphate,5-aminoallylcytidine-5′-triphosphate,5-aminoallyluridine-5′-triphosphate, 5-bromocytidine-5T-triphosphate,5-bromouridine-5′-triphosphate,5-Bromo-2T-deoxycytidine-5T-triphosphate,5-Bromo-2′-deoxyuridine-5′-triphosphate, 5-iodocytidine-5T-triphosphate,5-Iodo-2′-deoxycytidine-5′-triphosphate, 5-iodouridine-5′-triphosphate,5-Iodo-2T-deoxyuridine-5T-triphosphate,5-methylcytidine-5′-triphosphate, 5-methyluridine-5′-triphosphate,5-Propynyl-2′-deoxycytidine-5′-triphosphate,5-Propynyl-2′-deoxyuridine-5′-tri phosphate, 6-azacytidine-5′-triphosphate, 6-aza uridine-5′-triphosphate,6-chloropurineriboside-5′-triphosphate,7-deazaadenosine-5′-triphosphate, 7-deazaguanosine-5′-triphosphate,8-azaadenosine-5′-triphosphate, 8-azidoadenosine-5′-triphosphate,benzimidazole-riboside-5′-triphosphate,N1-methyladenosine-5T-triphosphate, N1-methylguanosine-5′-tri phosphate,N 6-methyladenosine-5′-tri phosphate,06-methylguanosine-5′-triphosphate, pseudouridine-5′-triphosphate, orpuromycin-5′-triphosphate, xanthosine-5′-triphosphate. Particularpreference is given to nucleotides for base modifications selected fromthe group of base-modified nucleotides consisting of5-methylcytidine-5′-tri phosphate, 7-deazaguanosine-5′-triphosphate,5-bromocytidine-5T-triphosphate, and pseudouridine-5′-triphosphate.

In some embodiments, modified nucleosides include pyridin-4-oneribonucleoside, 5-aza-uridine, 2-thio-5-aza-uridine, 2-thiouridine,4-thio-pseudouridine, 2-thio-pseudouridine, 5-hydroxyuridine,3-methyluridine, 5-carboxymethyl-uridine, 1-carboxymethyl-pseudouridine,5-propynyl-uridine, 1-propynyl-pseudouridine, 5-taurinomethyluridine,1-taurinomethyl-pseudouridine, 5-taurinomethyl-2-thio-uridine,1-taurinomethyl-4-thio-uridine, 5-methyl-uridine,1-methyl-pseudouridine, 4-thio-1-methyl-pseudouridine,2-thio-1-methyl-pseudouridine, 1-methyl-1-deaza-pseudouridine,2-thio-1-methyl-1-deaza-pseudouridine, dihydrouridine,dihydropseudouridine, 2-thio-dihydrouridine,2-thio-dihydropseudouridine, 2-methoxyuridine, 2-methoxy-4-thio-uridine,4-methoxy-pseudouridine, and 4-methoxy-2-thio-pseudouridine.

In some embodiments, modified nucleosides include 5-aza-cytidine,pseudoisocytidine, 3-methyl-cytidine, N4-acetylcytidine,5-formylcytidine, N4-methylcytidine, 5-hydroxymethylcytidine,1-methyl-pseudoisocytidine, pyrrolo-cytidine, pyrrolo-pseudoisocytidine,2-thio-cytidine, 2-thio-5-methyl-cytidine, 4-thio-pseudoisocytidine,4-thio-1-methyl-pseudoisocytidine,4-thio-1-methyl-1-deaza-pseudoisocytidine,1-methyl-1-deaza-pseudoisocytidine, zebularine, 5-aza-zebularine,5-methyl-zebularine, 5-aza-2-thio-zebularine, 2-thio-zebularine,2-methoxy-cytidine, 2-methoxy-5-methyl-cytidine,4-methoxy-pseudoisocytidine, and 4-methoxy-l-methyl-pseudoisocytidine.

In other embodiments, modified nucleosides include 2-aminopurine, 2,6-diaminopurine, 7-deaza-adenine, 7-deaza-8-aza-adenine,7-deaza-2-aminopurine, 7-deaza-8-aza-2-aminopurine,7-deaza-2,6-diaminopurine, 7-deaza-8-aza-2,6-diaminopurine,1-methyladenosine, N6-methyladenosine, N6-isopentenyladenosine,N6-(cis-hydroxyisopentenyl)adenosine,2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine,N6-glycinylcarbamoyladenosine, N6-threonylcarbamoyladenosine,2-methylthio-N6-threonyl carbamoyladenosine, N6,N6-dimethyladenosine,7-methyladenine, 2-methylthio-adenine, and 2-methoxy-adenine.

In other embodiments, modified nucleosides include inosine,1-methyl-inosine, wyosine, wybutosine, 7-deaza-guanosine,7-deaza-8-aza-guanosine, 6-thio-guanosine, 6-thio-7-deaza-guanosine,6-thio-7-deaza-8-aza-guanosine, 7-methyl-guanosine,6-thio-7-methyl-guanosine, 7-methylinosine, 6-methoxy-guanosine,1-methylguanosine, N2-methylguanosine, N2,N2-dimethylguanosine,8-oxo-guanosine, 7-methyl-8-oxo-guanosine, 1-methyl-6-thio-guanosine,N2-methyl-6-thio-guanosine, and N2,N2-dimethyl-6-thio-guanosine.

In some embodiments, the nucleotide can be modified on the major grooveface and can include replacing hydrogen on C-5 of uracil with a methylgroup or a halo group.

In specific embodiments, a modified nucleoside is5′-0-(I-Thiophosphate)-Adenosine, 5′-0-(1-Thiophosphate)-Cytidine,5′-0-(1-Thiophosphate)-Guanosine, 5′-0-(1-Thiophosphate)-Uridine or5′-0-(I-Thiophosphate)-Pseudouridine.

In further specific embodiments the modified nucleotides includenucleoside modifications selected from 6-aza-cytidine, 2-thio-cytidine,

-thio-cytidine, Pseudo-iso-cytidine, 5-aminoallyl-uridine,5-iodo-uridine, N1-methyl-pseudouridine, 5,6-dihydrouridine,

-thio-uridine, 4-thio-uridine, 6-aza-uridine, 5-hydroxy-uridine,deoxy-thymidine, 5-methyl-uridine, Pyrrolo-cytidine, inosine,

-thio-guanosine, 6-methyl-guanosine, 5-methyl-cytdine, 8-oxo-guanosine,7-deaza-guanosine, N1-methyl-adenosine, 2-amino-6-Chloro-purine,N6-methyl-2-amino-purine, Pseudo-iso-cytidine, 6-Chloro-purine,N6-methyl-adenosine,

-thio-adenosine, 8-azido-adenosine, 7-deaza-adenosine.

Further modified nucleotides have been described previously(WO2013052523).

In some embodiments of the present invention, the modified mRNAobtainable by the method according to the invention does not compriseany modified nucleosides as described above. In these embodiments, themodified mRNA preferably comprises exclusively nucleosides, which areselected from the group consisting of adenosine, cytosine, guanosine anduridine. Preferably, the modified mRNA is modified only with respect toits G and/or C content as described herein, wherein (non-modified)cytosine or guanosine replaces other nucleosides in order to increasethe G and/or C content as described herein.

Preferably, the modified mRNA that is obtainable by the method accordingto the invention has not been modified with a chemical modification atthe 4-, 5- or 6-position of the pyrimidine base of the nucleosides ofcytidine and/or uridine; a chemical modification at the 2-, 6-, 7- or8-position of the purine base of the nucleosides of adenosine, inosineand/or guanosine; and/or a chemical modification at the 2′-position ofthe sugar of the nucleosides of adenosine, inosine, guanosine, cytidineand/or uridine.

More preferably, the modified mRNA that is obtainable by the methodaccording to the invention has not been modified with a chemicalmodification at the 2-, 6-, 7- or 8-position of the purine base of thenucleosides of adenosine, inosine and/or guanosine; and a chemicalmodification at the 2′-position of the sugar of the nucleosides ofadenosine, inosine, guanosine, cytidine and/or uridine.

Even more preferably, the modified mRNA that is obtainable by the methodaccording to the invention has not been modified with a chemicalmodification at the 4-, 5-or 6-position of the pyrimidine base of thenucleosides of cytidine and/or uridine; and a chemical modification atthe 2′-position of the sugar of the nucleosides of adenosine, inosine,guanosine, cytidine and/or uridine.

Preferably, the modified mRNA that is obtainable by the method accordingto the invention has not been modified with a chemical modification atthe 5- or 6-position of the pyrimidine base of the nucleosides cytidineand/or uridine, wherein the chemical modification is preferably selectedfrom the group consisting of 4-thio, 5-iodo-/(5-I—), 5-bromo-/(5-Br—),5-aminoallyl-, 5-fluoro-/(5-F—), 5-hydroxy-, 5-hydro-/(5-H—), 5-nitro-,5-propynyl-/(5-(C

C—CH3)-), 5-methyl-, 5-methyl-2-thio-, 5-formyl-, 5-hydroxymethyl-,5-methoxy-, 5-oxyacetic acid methyl ester-, 5-oxyacetic acid-,5-carboxyhydroxymethyl-, 5-(carboxyhydroxymethyl)pyrimidine methylester-, 5-methoxycarbonylmethyl-, 5-methoxycarbonylmethyl-2-thio,5-aminomethyl-, 5-aminomethyl-2-thio-, 5-aminomethyl-2-seleno-,5-methylaminomethyl-, 5-carbamoylmethyl-, 5-carboxymethylaminomethyl-,5-carboxymethylaminomethyl-2-thio-, 5-carboxymethyl-, 5-methyldihydro-,5-taurinomethyl-, 5-taurinomethyl-2-thiouridine,5-isopentenylaminomethyl-, 5-isopentenylaminomethyl-2-thio-,5-aminopropyl-/(5-(C3H6NH3)-),5-methoxy-ethoxy-methyl-/(5-(CH2-O—C2H4-O—CH3)-) and 6-aza-.

Further, the modified mRNA that is obtainable by the method according tothe invention has preferably not been modified with a chemicalmodification at the 2-, 6-, 7- or 8-position of the purine base of thenucleosides adenosine, inosine and/or guanosine, wherein the chemicalmodification is preferably selected from the group consisting of2-Amino-, 7-Deaza-, 8-Aza- and 8-Azido-.

In addition or alternatively, the modified mRNA that is obtainable bythe method according to the invention has preferably not been modifiedwith a chemical modification at the 2′-position of the sugar of thenucleosides adenosine, inosine, guanosine, cytidine and/or uridine, whenincorporated in the RNA sequence, wherein such chemical modifications atthe 2′-position of the sugar of the nucleosides adenosine, inosine,guanosine, cytidine and/or uridine may be selected from the groupconsisting of 2′-deoxy-, 2′-amino-2′-deoxy-/2′-amino-,2′-fluoro-2′-deoxy-/2′-fluoro- and 2′-O-methyl-2′-deoxy-/2′-O-methyl-.

Preferably, the modified mRNA that is obtainable by the method accordingto the invention has not been modified with a chemical modification atthe 4,-5- or 6-position of the base pyrimidine of the nucleosidescytidine and/or uridine and at the 2′-position of the ribose sugar asdefined above, wherein the chemical modification is preferably selectedfrom the group consisting of 4-thio-2′-deoxy-, 4-thio-2′-amino-,4-thio-2′-fluoro-, 4-thio-2′-O-methyl-, 5-iodo-2′-deoxy-,5-iodo-2′-amino-, 5-iodo-2′-fluoro-, 5-iodo-2′-O-methyl-,5-bromo-2′-deoxy-, 5-bromo-2′-amino-, 5-bromo-2′-fluoro-,5-bromo-2′-O-methyl-, 5-aminoallyl-2′-deoxy-, 5-aminoallyl-2′-amino-,5-aminoallyl-2′-fluoro-, 5-aminoallyl-2′-O-methyl-, 5-fluoro-2′-deoxy-,5-fluoro-2′-amino-, 5-fluoro-2′-fluoro-, 5-fluoro-2′-O-methyl-,5-hydroxy-2′-deoxy-, 5-hydroxy-2′-amino-, 5-hydroxy-2′-fluoro-,5-hydroxy-2′-O-methyl-, 5-hydro-2′-deoxy-, 5-hydro-2′-amino-,5-hydro-2′-fluoro-, 5-hydro-2′-O-methyl-, 5-nitro-2′-deoxy-,5-nitro-2′-amino-, 5-nitro-2′-fluoro-, 5-nitro-2′-O-methyl-,5-propynyl-2′-deoxy-, 5-propynyl-2′-amino-, 5-propynyl-2′-fluoro-,5-propynyl-2′-O-methyl-, 5-methyl-2′-deoxy-, 5-methyl-2′-amino-,5-methyl-2′-fluoro-, 5-methyl-2′-O-methyl (5,2′-O-dimethyl)-,5-methyl-2-thio-2′-deoxy-, 5-methyl-2-thio-2′-amino-,5-methyl-2-thio-2′-fluoro-, 5-methyl-2-thio-2′-O-methyl-,5-formyl-2′-deoxy-, 5-formyl-2′-amino-, 5-formyl-2′-fluoro-,5-formyl-2′-O-methyl-, 5-hydroxymethyl-2′-deoxy-,5-hydroxymethyl-2′-amino-, 5-hydroxymethyl-2′-fluoro-,5-hydroxymethyl-2′-O-methyl-, 5-methoxy-2′-deoxy-, 5-methoxy-2′-amino-,5-methoxy-2′-fluoro-, 5-methoxy-2′-O-methyl-, 5-oxyacetic acid methylester-2′-deoxy-, 5-oxyacetic acid methyl ester-2′-amino-, 5-oxyaceticacid methyl ester-2′-fluoro-, 5-oxyacetic acid methylester-2′-O-methyl-, 5-oxyacetic acid-2′-deoxy-, 5-oxyaceticacid-2′-amino-, 5-oxyacetic acid-2′-fluoro-, 5-oxyaceticacid-2′-O-methyl-, 5-carboxyhydroxymethyl-2′-deoxy-,5-carboxyhydroxymethyl-2′-amino-, 5-carboxyhydroxymethyl-2′-fluoro-,5-carboxyhydroxymethyl-2′-O-methyl-, 5-(carboxyhydroxymethyl)pyrimidinemethyl ester-2′-deoxy-, 5-(carboxyhydroxymethyl)pyrimidine methylester-2′-amino-, 5-(carboxyhydroxymethyl)pyrimidine methylester-2′-fluoro-, 5-(carboxyhydroxymethyl)pyrimidine methylester-2′-O-methyl-, 5-methoxycarbonylmethyl-2′-deoxy-,5-methoxycarbonylmethyl-2′-amino-, 5-methoxycarbonylmethyl-2′-fluoro-,5-methoxycarbonylmethyl-2′-O-methyl-, 5-methoxycarbonylmethyl-2-thio2′-deoxy-, 5-methoxycarbonylmethyl-2-thio 2′-amino-,5-methoxycarbonylmethyl-2-thio 2′-fluoro-,5-methoxycarbonylmethyl-2-thio 2′-O-methyl-, 5-aminomethyl-2′-deoxy-,5-aminomethyl-2′-amino-, 5-aminomethyl-2′-fluoro-,5-aminomethyl-2′-O-methyl-, 5-aminomethyl-2-thio-2′-deoxy-,5-aminomethyl-2-thio-2′-amino-, 5-aminomethyl-2-thio-2′-fluoro-,5-aminomethyl-2-thio-2′-O-methyl-, 5-aminomethyl-2-seleno-2′-deoxy-,5-aminomethyl-2-seleno-2′-amino-, 5-aminomethyl-2-seleno-2′-fluoro-,5-aminomethyl-2-seleno-2′-O-methyl-, 5-methylaminomethyl-2′-deoxy-,5-methylaminomethyl-2′-amino-, 5-methylaminomethyl-2′-fluoro-,5-methylaminomethyl-2′-O-methyl-, 5-carbamoylmethyl-2′-deoxy-,5-carbamoylmethyl-2′-amino-, 5-carbamoylmethyl-2′-fluoro-,5-carbamoylmethyl-2′-O-methyl-, 5-carboxymethylaminomethyl-2′-deoxy-,5-carboxymethylaminomethyl-2′-amino-,5-carboxymethylaminomethyl-2′-fluoro-,5-carboxymethylaminomethyl-2′-O-methyl-,5-carboxymethylaminomethyl-2-thio-2′-deoxy-,5-carboxymethylaminomethyl-2-thio-2′-amino-,5-carboxymethylaminomethyl-2-thio-2′-fluoro-,5-carboxymethylaminomethyl-2-thio-2′-O-methyl-,5-carboxymethyl-2′-deoxy-, 5-carboxymethyl-2′-amino-,5-carboxymethyl-2′-fluoro-, 5-carboxymethyl-2′-O-methyl-,5-methyldihydro-2′-deoxy-, 5-methyldihydro-2′-amino-,5-methyldihydro-2′-fluoro-, 5-methyldihydro-2′-O-methyl-,5-taurinomethyl-2′-deoxy-, 5-taurinomethyl-2′-amino-,5-taurinomethyl-2′-fluoro-, 5-taurinomethyl-2′-O-methyl-,5-taurinomethyl-2-thiouridine-2′-deoxy-,5-taurinomethyl-2-thiouridine-2′-amino-,5-taurinomethyl-2-thiouridine-2′-fluoro-,5-taurinomethyl-2-thiouridine-2′-O-methyl-,5-isopentenylaminomethyl-2′-deoxy-, 5-isopentenylaminomethyl-2′-amino-,5-isopentenylaminomethyl-2′-fluoro-,5-isopentenylaminomethyl-2′-O-methyl-,5-isopentenylaminomethyl-2-thio-2′-deoxy-,5-isopentenylaminomethyl-2-thio-2′-amino-,5-isopentenylaminomethyl-2-thio-2′-fluoro-,5-isopentenylaminomethyl-2-thio-2′-O-methyl-, 5-aminopropyl-2′-deoxy-,5-aminopropyl-2′-amino-, 5-aminopropyl-2′-fluoro-,5-aminopropyl-2′-O-methyl-, 5-methoxy-ethoxy-methyl-2′-deoxy-,5-methoxy-ethoxy-methyl-2′-amino-, 5-methoxy-ethoxy-methyl-2′-fluoro-,5-methoxy-ethoxy-methyl-2′-O-methyl-, 6-aza-2′-deoxy-, 6-aza-2′-amino-,6-aza-2′-fluoro- and 6-aza-2′-O-methyl-.

More preferably, the modified mRNA that is obtainable by the methodaccording to the invention has not been modified with a chemicalmodification at the 2-, 6-, 7- or 8-position of the purine base of thenucleosides adenosine, inosine and/or guanosine and at the 2′-positionof the ribose sugar as defined above, wherein the chemical modificationis selected from the group consisting of 2-Amino-2′-deoxy-,2-Amino-2′-amino-, 2-Amino-2′-fluoro-, 2-Amino-2′-O-methyl-,7-Deaza-2′-deoxy-, 7-Deaza-2′-amino-, 7-Deaza-2′-fluoro-,7-Deaza-2′-O-methyl-, 8-Aza-2′-deoxy-, 8-Aza-2′-amino-,8-Aza-2′-fluoro-, 8-Aza-2′-O-methyl-, 8-Azido-2′-deoxy-,8-Azido-2′-amino-, 8-Azido-2′-fluoro- and 8-Azido-2′-O-methyl-.

According to a further embodiment, the modified mRNA, which is obtainedaccording to one or more embodiments of the inventive method of targetedmodulation of the immune response against an mRNA, is devoid ofdestabilizing sequence elements (DSE) in the 3′ and/or 5′ UTR.

As used herein, the term “destabilizing sequence element” (DSE) refersto a sequence of nucleotides, which reduces the half-life of atranscript, e.g. the half-life of the inventive modified mRNA inside acell and/or organism, e.g. a human. Accordingly, a DSE comprises asequence of nucleotides, which reduces the intracellular half-life of anRNA transcript.

DSE sequences are found in short-lived mRNAs such as, for example;c-fos, c-jun, c-myc, GM-CSF, IL-3, TNF -alpha, IL-2, IL-6, IL-8, IL-10,Urokinase, bcl-2, SGLT1 (Na(+)-coupled glucose transporter), Cox-2(cyclooxygenase 2), IL8, PAI-2 (plasminogen activator inhibitor type 2),betal-adrenergic receptor, GAP43 (5′UTR and 3 ′UTR). AU-rich elements(ARES) and/or U-rich elements (UREs), including but not limited tosingle, tandem or multiple or overlapping copies of the nonamerUUAUUUA(U/A)(U/A) (where U/A is either an A or a U) and/or the pentamerAUUUA and/or the tetramer AUUU. Accordingly, the DNA template used forin vitro transcription of the modified mRNA according to the presentinvention are devoid of the corresponding sequences.

Assays for measuring RNA degradation, such as e.g. degradation of themodified mRNA of the invention and thus the stability of the inventivemodified mRNA are known in the art. For example, RNA half-life can bemeasured by the methods described by Duan and Jefcoate (Duan andJefcoate, 2007. J. Mol. Endocrinol. 38(1-2):159-79).

According to this method, cells may e.g. be plated in 12-well plates at25% density 24 hours prior to transfection. For transfection 1 μg ofmodified mRNA of the invention may be transfected per well. Thefollowing proportion may be used: 1 μg mRNA, 1 μl Translt-mRNA reagent,1 μl mRNA boost reagent and 100 μl serum-free media. The modified mRNAof the invention may then first be mixed with serum-free media, then RNAboost reagent may be added and mixed, followed by the addition oftransfection reagent. The mixture may then be incubated at roomtemperature for three minutes and aliqoted directly onto cells in, e.g.complete media. Twelve hours after transfection, when cell mRNA levelshave reached a steady state, cells may be washed once and cell culturemedium may be exchanged for complete medium devoid of the transfectionreagents (mixture) (zero hour time point). The degradation of themodified mRNA of the invention within the cells may then be determinedby harvesting cells at appropriate time points, such as e.g. 12 h and/or16 h and/or 18 h and/or 20 h and/or 24 and/or 48 h post transfection.Total cellular RNA may subsequently be isolated and the amount ofmodified mRNA of the invention may be determined by reversetranscription and/or quantitative real-time PCR using specific primersthat bind to the coding region of the modified mRNA of the inventionand/or the 5′ and/or 3′ UTRs of the modified mRNA. The half-life of themodified mRNA of the invention may then be calculated by linearregression fit of the time points on semi-log plots.

In a preferred embodiment the inventive modified mRNA may furthercomprise a 5′-CAP structure and/or a polyA-tail of at least 60nucleotides, more preferably of at least 70 nucleotides and/or a 3′stabilizing sequence.

Within the present invention the term “CAP structure” refers to astructure found on the 5′-end of an mRNA, such as e.g. the modified mRNAaccording to one or more embodiments of the method of present inventionand generally consists of a guanosine nucleotide connected to the mRNAvia an unusual 5′ to 5′ triphosphate linkage. The guanosine nucleotideis methylated on the 7-position directly after capping in vivo by amethyl transferase. It is referred to as a 7-methylguanylate cap,abbreviated m7G. Further modifications include the possible methylationof the 2′ hydroxy-groups of the first 2 ribose sugars of the 5′ end ofthe mRNA.

For an efficient translation of a given mRNA, such as e.g. the modifiedmRNA according to the invention, an effective binding of ribosomes tothe ribosome binding site, which is also referred to as “Kozak sequence”(5′-GCCGCCACCAUGG (SEQ ID NO: 11), wherein the AUG denotes the startcodon) is necessary. In this regard it has been established that anincreased A/U content around this site permits a more efficient ribosomebinding to the mRNA (Kozak, Mol Cell Biol. 1989 November;9(11):5073-80). Accordingly, the inventive modified mRNA may comprise aKozak sequence for more efficient ribosome binding to the mRNA. Theinventive modified mRNA may further comprise a poly-A tail, which is asequence of up to 200 adenosine nucleotides located at the 3′ end of themRNA.

According to a further embodiment of the present invention, theinventive modified mRNA may comprise in the 3′ non-translated region oneor more stabilisation sequences that are capable of increasing thehalf-life of the mRNA in the cytosol. These stabilisation sequences mayexhibit a 100% sequence homology with naturally occurring sequences thatare present in viruses, bacteria and eukaryotic cells, but may howeveralso be partly or completely synthetic. As an example of stabilisingsequences that may be used in the present invention, the non-translatedsequences (UTR) of the β-globin gene, for example of homo sapiens orxenopus laevis, may be mentioned. Another example of a stabilisationsequence has the general formula (C/U)CCANxCCC(U/A)PyxUC(C/U)CC (SEQ IDNO: 12), which is contained in the 3′UTR of the very stable mRNA thatcodes for α-globin, α-(I)-collagen, 15-lipoxygenase or for tyrosinehydroxylase (c.f. Holcik et al., Proc. Natl. Acad. Sci. USA 1997, 94:2410 to 2414). Such stabilisation sequences may be used individually orin combination with one another for stabilizing the inventive modifiedmRNA as well as in combination with other stabilisation sequences knownto the person skilled in the art.

According to a preferred embodiment, the present invention provides fora pharmaceutical composition comprising a modified mRNA according to oneor more of the above embodiments of the present invention, or theinventive modified mRNA according to one or more of the aboveembodiments. The pharmaceutical composition optionally comprises one ormore pharmaceutically acceptable excipients, carriers, diluents and/orvehicles.

The term “pharmaceutically acceptable” as used in connection with thepharmaceutical compositions of the invention, refers to molecularentities and compositions that are physiologically tolerable and do nottypically produce untoward reactions when administered to an individual,such as e.g. a human. Preferably, as used herein, the term“pharmaceutically acceptable” means approved by a regulatory agency ofthe Federal or a state government or listed in the U.S. Pharmacopeia orother generally recognized pharmacopeia for use in animals, and moreparticularly in humans.

The term “carrier” as used in connection with the pharmaceuticalcompositions of the invention refers to a diluent, adjuvant, excipient,or vehicle with which the compound is administered. Such pharmaceuticalcarriers can be sterile liquids, such as water and oils. Water oraqueous solution saline solutions and aqueous dextrose and glycerolsolutions are preferably employed as carriers, particularly forinjectable solutions. Suitable pharmaceutical carriers are described in“Remington's Pharmaceutical Sciences” by E. W. Martin, 18th Edition. Theterm “pharmaceutically acceptable” refers to the non-toxicity of amaterial which does not interact with the action of the activecomponent, i.e. with the action of the inventive modified mRNA of thepharmaceutical composition.

Suitable excipients and/or vehicles for use with the pharmaceuticalcomposition of the present invention are, for example, water, saline,dextrose, glycerol, ethanol, or the like, and combinations thereof. Inaddition, if desired, the vehicle may contain minor amounts of auxiliarysubstances such as wetting or emulsifying agents or pH buffering agents.Actual methods of preparing such dosage forms are known, or will beapparent, to those skilled in the art, such as those, e.g. which aredisclosed in e.g., Remington's Pharmaceutical Sciences, Mack PublishingCompany, Easton, Pennsylvania, 17th edition, 1985; Remington: TheScience and Practice of Pharmacy, A. R. Gennaro, (2000) Lippincott,Williams & Wilkins. A non-limiting list of commonly used and acceptedexcipients is also provided in “VOLUME 3B Guidelines Medicinal productsfor human use Safety, environment and information Excipients in thelabel and package leaflet of medicinal products for human use, July2003” issued by the European Commission, which is hereby incorporated inits entirety into the disclosure of this invention. The composition orformulation to be administered will, in any event, contain a quantity ofthe agent adequate to achieve the desired state in the subject beingtreated.

Possible carrier substances for use with the pharmaceutical compositionof the present invention for parenteral administration are e.g. sterilewater, sterile sodium chloride solution, polyalkylene glycols,hydrogenated naphthalenes and, in particular, biocompatible lactidepolymers, lactide/glycolide copolymers orpolyoxyethylene/polyoxypropylene copolymers. The pharmaceuticalcomposition according to may further comprise filler substances orsubstances such as lactose or mannitol. Preferred carriers for use inthe inventive pharmaceutical composition are typically aqueous carriermaterials, water for injection (WFI) or water buffered with phosphate,citrate, HEPES or acetate etc. being used, and the pH is typicallyadjusted to 5.0 to 8.0, preferably 6.5 to 7.5. The carrier or thevehicle will additionally preferably comprise salt constituents, e.g.sodium chloride, potassium chloride or other components which render thesolution e.g. isotonic. Furthermore, the carrier or the vehicle cancontain, in addition to the abovementioned constituents, additionalcomponents, such as human serum albumin (HSA), polysorbate 80, sugars oramino acids.

In a more preferred embodiment the present invention provides for apharmaceutical composition comprising the modified mRNA according to oneor more embodiments of the inventive method for use in the treatment ofdiseases amenable to protein replacement therapy, e.g. for the treatmentof hereditary or endocrinological diseases, preferably for use in thetreatment of diseases caused by amino acid disorders, carbohydratemetabolism disorders, cholesterol biosynthesis disorders, fatty acidoxidation defects and fat metabolism disorders, lactic acidosis,glycogen storage diseases, mitochondrial disorders, organic aciddisorders, urea cycle disorders, lysosomal storage disease disorders.

The term “protein replacement therapy” as used herein refers to theintroduction of an mRNA, such as e.g. the modified of the invention intoan individual having a deficiency in a protein encoded by the modifiedmRNA according to the invention, i.e. an mRNA modified by the inventivemethod of targeted modulation of the immune response against said mRNAcoding for at least one biologically active polypeptide or protein.

Accordingly, the pharmaceutical composition of the invention, whichcomprises the modified mRNA according to one or more embodiments of theinventive method may be used in the treatment of diseases or in aidingin the treatment of the diseases which are characterized by a proteindeficiency.

The term “diseases which are characterized by a protein deficiency ” asused in the context of the present invention, such as e.g. in thecontext of the pharmaceutical composition comprising the modified mRNAof the invention refers to any disorder that presents with a pathologycaused by absent or insufficient amounts of a protein. This termencompasses protein folding disorders, i.e., conformational disorders,that result in a biologically inactive protein product. Proteininsufficiency can be involved in infectious diseases, immunosuppression,organ failure, glandular problems, radiation illness, nutritionaldeficiency, poisoning, or other environmental or external insults.

There are currently about 1100 known inherited disorders characterizedby protein deficiency or loss-of-function in specific tissue. Thesedisorders may be treatable by protein replacement therapy in theory,e.g. the method of the present invention contemplates therapy forproteins currently suited for use in protein replacement therapy that isavailable now or will be in the future. In such disorders, certain cellsor all of the cells of an individual lack a sufficient functionalprotein, contain an inactive form of the protein or contain insufficientlevels for biological function.

Further, the list of diseases identified as being conformationaldisorders, caused by mutations that alter protein folding andretardation of the mutant protein in the ER, resulting in proteindeficiency, is increasing. These include cystic fibrosis, α1-antitrypsindeficiency, familial hypercholesterolemia, Fabry disease, Alzheimer'sdisease (Selkoe, Annu. Rev. Neurosci. 1994; 17:489-517), osteogenesisimperfecta (Chessler et al., J. Biol. Chem. 1993; 268:18226-18233),carbohydrate-deficient glycoprotein syndrome (Marquardt et al., Eur. J.Cell. Biol. 1995; 66: 268-273), Maroteaux-Lamy syndrome (Bradford etal., Biochem. J. 1999; 341:193-201), hereditary blindness (Kaushal etal., Biochemistry 1994; 33:6121-8), Glanzmann thrombasthenia (Kato etal., Blood 1992; 79:3212-8), hereditary factor VII deficiency (Arbini etal., Blood 1996; 87:5085-94), oculocutaneous albinism (Halaban et al.,Proc. Natl. Acad. Sci. USA. 2000; 97:5889-94) and protein C deficiency(Katsumi, et al., Blood 1996; 87:4164-75). Recently, one mutation in theX-linked disease adrenoleukodystrophy (ALD), resulted in misfolding ofthe defective peroxisome transporter which could be rescued bylow-temperature cultivation of affected cells (Walter et al., Am J HumGenet 2001; 69:35-48). It is generally accepted that mutations takeplace evenly over the entire sequence of a gene. Therefore, it ispredictable that the phenotype resulting from misfolding of thedeficient protein exists in many other genetic disorders.

Many of the inherited protein deficient disorders are enzymedeficiencies. As indicated above, a large class of inherited-enzymedisorders involves mutations in lysosomal enzymes and are referred to aslysosomal storage disorders (LSDs). Lysosomal storage disorders are agroup of diseases caused by the accumulation of glycosphingolipids,glycogen, mucopolysaccharides Examples of lysosomal disorders includebut are not limited to Gaucher disease (Beutler et al., The Metabolicand Molecular Bases of Inherited Disease, 8th ed. 2001 Scriver et al.,ed. pp. 3635-3668, McGraw-Hill, New York), GM1-gangliosidosis (id. at pp3775-3810), fucosidosis (The Metabolic and Molecular Bases of InheritedDisease 1995. Scriver, C. R., Beaudet, A. L., Sly, W. S. and Valle, D.,ed pp. 2529-2561, McGraw-Hill, New York), mucopolysaccharidoses (id. atpp 3421-3452), Pompe disease (id. at pp. 3389-3420), Hurler-Scheiedisease (Weismann et al., Science 1970; 169, 72-74), Niemann-Pick A andB diseases, (The Metabolic and Molecular Bases of Inherited Disease 8thed. 2001. Scriver et al. ed., pp 3589-3610, McGraw-Hill, Now York), andFabry disease (id. at pp. 3733-3774).

Fabry disease is an X-linked inborn error of glycosphingolipidmetabolism caused by deficient lysosomal α-galactosidase A (α-Gal A)activity (Desnick et al., The Metabolic and Molecular Bases of InheritedDisease, 8th Edition Scriver et al. ed., pp. 3733-3774, McGraw-Hill, NewYork 2001;

Brady et al., N. Engl. J. Med. 1967; 276,1163-1167). This enzymaticdefect leads to the progressive deposition of neutral glycosphingolipidswith α-galactosyl residues, predominantly globotriaosylceramide (GL-3),in body fluids and tissue lysosomes. The frequency of the disease isestimated to be about 1:40,000 in males, and is reported throughout theworld within different ethnic groups. In classically affected males, theclinical manifestations include angiokeratoma, acroparesthesias,hypohidrosis, and characteristic corneal and lenticular opacities (TheMetabolic and Molecular Bases of Inherited Disease, 8th Edition 2001,Scriver et al., ed., pp. 3733-3774, McGraw-Hill, New York). The affectedmale's life expectancy is reduced, and death usually occurs in thefourth or fifth decade as a result of vascular disease of the heart,brain, and/or kidneys. In contrast, patients with the milder “cardiacvariant” normally have 5-15% of normal α-Gal A activity, and presentwith left ventricular hypertrophy or a cardiomyopathy. These cardiacvariant patients remain essentially asymptomatic when their classicallyaffected counterparts are severely compromised. Recently, cardiacvariants were found in 11% of adult male patients with unexplained leftventricular hypertrophic cardiomyopathy, suggesting that Fabry diseasemay be more frequent than previously estimated (Nakao et aL, N. Engl. J.Med. 1995; 333: 288-293). The α-Gal A gene has been mapped to Xq22,(Bishop et al., Am. J. Hum. Genet. 1985; 37: A144), and the full-lengthcDNA and entire 12-kb genomic sequences encoding α-Gal A have beenreported (Calhoun et al., Proc. Natl. Acad Sci. USA 1985; 82: 7364-7368;Bishop et al., Proc. Natl. Acad. Sci. USA 1986; 83: 4859-4863; Tsuji etal., Bur. J. Biochem. 1987; 165: 275-280; and Kornreich et al., NucleicAcids Res. 1989; 17: 3301-3302). There is a marked genetic heterogeneityof mutations that cause Fabry disease (The Metabolic and Molecular Basesof Inherited Disease, 8th Edition 2001, Scriver et al., ed, pp.3733-3774, McGraw-Hill, New York; Eng et al., Am. J. Hum. Genet. 1993;53: 1186-1197; Eng et al., Mol. Med. 1997; 3:174-182; and Davies et al.,Bur. J. Hum. Genet. 1996; 4: 219-224). To date, a variety of missense,nonsense, and splicing mutations, in addition to small deletions andinsertions, and larger gene rearrangements have been reported.

Gaucher disease is a deficiency of the lysosomal enzymeβ-glucocerebrosidase that breaks down fatty glucocerebrosides. The fatthen accumulates, mostly in the liver, spleen and bone marrow. Gaucherdisease can result in pain, fatigue, jaundice, bone damage, anemia andeven death. There are three clinical phenotypes of Gaucher disease.Patients with, Type 1 manifest either early in life or in youngadulthood, bruise easily and experience fatigue due to anemia, low bloodplatelets, enlargement of the liver and spleen, weakening of theskeleton, and in some instances have lung and kidney impairment. Thereare no signs of brain involvement. In Type II, early-onset, liver andspleen enlargement occurs by 3 months of age and there is extensivebrain involvement. There is a high mortality rate by age 2. Type III ischaracterized by liver and spleen enlargement and brain seizures. Theβ-glucocerebrosidase gene is located on the human 1q21 chromosome. Itsprotein precursor contains 536 amino acids and its mature protein is 497amino acids long.

Gaucher disease is considerably more common in the descendants of Jewishpeople from Eastern Europe (Ashkenazi), although individuals from anyethnic group may be affected. Among the Ashkenazi Jewish population,Gaucher disease is the most common genetic disorder, with an incidenceof approximately 1 in 450 persons. In the general public, Gaucherdisease affects approximately 1 in 100,000 persons. According to theNational Gaucher Foundation, 2,500 Americans suffer from Gaucherdisease.

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most commonX-linked human enzyme deficiency. The G6PD enzyme catalyzes anoxidation/reduction reaction that is essential for the production ofribose, which is an essential component of both DNA and RNA. G6PD alsoinvolved in maintaining adequate levels of NADPH inside the cell. NADPHis a required cofactor in many biosynthetic reactions. Individuals withthis deficiency have clinical symptoms including neonatal jaundice,abdominal and/or back pain, dizziness, headache, dyspnea (irregularbreathing), and palpitations.

Additional examples of diseases amenable to protein replacement therapy,which may be treated with the pharmaceutical composition of the presentinvention, e.g. a pharmaceutical composition comprising a modified mRNAaccording to one or more of the embodiments of the present invention,include

lysosomal storage disease disorders, such as, e.g. activatordeficiency/GM2, gangliosidosis, alpha-mannosidosis,aspartylglucosaminuria, cholesteryl ester storage disease, chronicHexosaminidase A deficiency, cystinosis, Danon disease, Farber disease,fucosidosis, galactosialidosis, Gaucher DiseaseType I, II, III; GM1gangliosidosis, Infantile/late infantile/juvenile/adult/chronic I-Celldisease/Mucolipidosis II, infantile Free Sialic Acid StorageDisease/ISSD, juvenile hexosaminidase A deficiency, Krabbe disease,infantile onset/late onset lysosomal acid lipase deficiency, earlyonset/late onset metachromatic Leukodystrophy, mucopolysaccharidosesdisorders, pseudo-Hurler polydystrophy/Mucolipidosis IIIA, MPSI HurlerSyndrome, MPSI Scheie Syndrome, MPS I Hurler-Scheie Syndrome, MPS IIHunter syndrome, Sanfilippo syndrome Type A/MPS III A, Sanfilipposyndrome Type B/MPS III B, Sanfilippo syndrome Type C/MPS III C,Sanfilippo syndrome Type D/MPS III D, Morquio Type A/MPS IVA, MorquioType B/MPS IVB, MPS IX Hyaluronidase Deficiency, MPS VI Maroteaux-Lamy,MPS VII Sly Syndrome, Mucolipidosis I/Sialidosis, Mucolipidosis IIIC,Mucolipidosis type IV, Multiple sulfatase deficiency, Niemann-PickDisease, Type A/Type B/Type C neuronal ceroid lipofuscinoses, CLN6disease, atypical late infantile/late onset variant/early juvenileBatten-Spielmeyer-Vogt/Juvenile NCL/CLN3 disease, Finnish Variant LateInfantile CLN5, Jansky-Bielschowsky disease/Late infantile CLN2/TPP1Disease, Kufs/Adult-onset NCL/CLN4 disease, Northern Epilepsy/variantlate infantile CLN8, Santavuori-Haltia/Infantile CLN1/PPT disease,beta-mannosidosis, Pompe disease/Glycogen storage disease type II,pycnodysostosis, Sandhoff disease/Adult Onset/GM2 gangliosidosis,Sandhoff disease/GM2 gangliosidosis—Infantile, Sandhoff disease/GM2gangliosidosis—Juvenile, Schindler disease, Salla disease/Sialic AcidStorage Disease, Tay-Sachs/GM2 gangliosidosis, Wolman disease, and/or

amino acid metabolism disorders, such as, e.g. alkaptonuria,aspartylglucosaminuria, methylmalonic acidemia, maple syrup urinedisease, homocystinuria, tyrosinemia, trimethylaminuria, Hartnupdisease, biotinidase deficiency, ornithine carbamoyltransferasedeficiency, carbamoyl-phosphate synthase I deficiency disease,citrullinemia, hyperargininemia, hyperhomocysteinemia,hypermethioninemia, hyperlysinemias, nonketotic hyperglycinemia,propionic acidemia, hyperprolinemia, and/or

carbohydrate metabolism disorders, such as e.g. lactose intolerance,other disorders of carbohydrate metabolism, glycogen storage disease,glycogen storage disease type I (von

Gierke's disease), glycogen storage disease type II (Pompe's disease),glycogen storage disease type III, glycogen storage disease type IV,glycogen storage disease type V (McArdle's disease), disorders offructose metabolism, essential fructosuria, fructose-1,6-diphosphatasedeficiency, hereditary fructose intolerance, disorders of galactosemetabolism,

galactosaemia, galactokinase deficiency, disorders of intestinalcarbohydrate absorption, e.g. glucose-galactose malabsorption, sucrasedeficiency, disorders of pyruvate metabolism and gluconeogenesis, e.g.deficiency of phosphoenolpyruvate carboxykinase, deficiency of pyruvatecarboxylase, deficiency of pyruvate dehydrogenase, other disorders ofcarbohydrate metabolism, such as, e.g. essential pentosuria, oxalosis,oxaluria, renal glycosuria, and/or

lipid and cholesterol biosynthesis disorders, such as, e.g. purehypercholesterolaemia, familial hypercholesterolaemia, Fredrickson'shyperlipoproteinaemia, type Ila, hyperbetalipoproteinaemia,hyperlipidaemia, group A, low-density-lipoprotein-type (LDL)hyperlipoproteinaemia, hyperglyceridaemia, endogenoushyperglyceridaemia, Fredrickson's hyperlipoproteinaemia, type IV,hyperlipidaemia, group B, hyperprebetalipoproteinaemiavery-low-density-lipoprotein-type (VLDL) hyperlipoproteinaemia, and/or

lactic acidosis caused by e.g. glucose-6-phosphatase deficiency,fructose 1,6-diphosphatase deficiency, pyruvate dehydrogenasedeficiency, pyruvate carboxylase deficiency, and/or glycogen storagediseases (GSDs), e.g. GSD type I, GSD type II, GSD type III, GSD typeIV, GSD type V, GSD type VI, GSD type VII, GSD type VIII, GSD type IX,GSD type X, GSD type XI, and/or mitochondrial disorders, such as, e.g.Kearns-Sayre syndrome, mitochondrial encephalopathy, lactic acidosis andstroke-like episodes (MELAS syndrome), mitochondrialneurogastrointestinal encephalopathy syndrome (MNGIE), myoclonus withepilepsy and with ragged red fibers (MERRF syndrome), neuropathy,ataxia, and retinitis pigmentosa (NARP syndrome), and/or organic aciddisorders, such as, e.g. glutaric acidemia type 1, type 2,hyperlysinemia, pipecolic acidemia, saccharopinuria, and/or urea cycledisorders, such as, e.g. citrullinemia, hyperammonemia.

In addition to inherited disorders, the pharmaceutical compositionaccording to the invention may be used in and/or used in aiding in thetreatment of other enzyme deficiencies, which arise from damage to atissue or organ resulting from primary or secondary disorders. Forexample, damaged pancreatic tissue, or pancreatitis, is caused byalcoholism results in a deficiency in pancreatic enzymes necessary fordigestion. Pancreatitis is currently being treated using enzymereplacement therapy.

In addition to disorders characterized by protein deficiencies, somedisorders may be treated by the pharmaceutical composition of thepresent invention to replace proteins in order to enhance or stimulatebiological processes. For example, currently individuals with anemia areadministered recombinant erythropoietin (EPOGEN®, PROCRIT®, EPOIETIN®)to stimulate red blood cell production and increase oxygentransportation to tissues. In addition, recombinant interferons such asinterferon alpha 2b (INTRON A®, PEG-INTRON®, or REBETOL®), andinterferon beta 1a (AVONEX®, BETASERON®) are administered to treathepatitis B and multiple sclerosis, respectively. Still other proteinsadministered are recombinant human deoxyribonuclease I(rhDNase-)PULMOZYME®), an enzyme which selectively cleaves DNA used toimprove pulmonary function in patients with cystic fibrosis; recombinantthyroid stimulating hormone (THYROGEN®) developed for use in thyroidcancer patients who have had near-total or total thyroidectomy, and whomust therefore take thyroid hormones; recombinant G-CSF (NEUPOGEN®) fortreating neutropenia from chemotherapy, and digestive enzymes inindividuals with pancreatitis. Thus, the pharmaceutical composition ofthe present invention may be used in the treatment of the abovementioned conditions.

Additionally, the the pharmaceutical composition according to theinvention may be used in the treatment of and/or used in aiding in thetreatment of growth hormone deficiency, such as e.g. pituitary-relatedgrowth hormone deficiency, growth hormone releasing hormone (GHRH)deficiency. Accordingly, the pharmaceutical composition according to thepresent invention may be used in treating or aiding in the treatment ofthe above diseases.

The pharmaceutical composition of the invention comprising the modifiedmRNA according to one or more embodiments of the inventive method mayalso be used in another area of protein replacement therapy, such as,e.g. in the treatment of infectious diseases and cancer with antibodies,which have a highly specific, well-defined active site. Accordingly, thepharmaceutical composition of the invention may comprise a modified mRNAof the invention, which codes for an antibody for use in the treatmentof cancer or infectious diseases. The antibodies encoded by the modifiedmRNA of the invention comprised in the pharmaceutical composition may bee.g. any type of antibody, however, in a preferred embodiment theencoded antibody is a single chain Fv fragments (scFv), preferably anintrabody.

The term “intrabody” or “intrabodies” as used herein refers tointracellularly expressed antibodies. For example, whole antibodies,heavy chains, Fab′ fragments, single chain antibodies and diabodies canbe used as intrabodies, preferably the intrabody is a single chainantibody.

The pharmaceutical composition comprising a modified mRNA of theinvention, which codes for an antibody, such as, e.g. a single-chain Fvfragments (scFv) may be administered to a patient in need thereof,preferably a therapeutically effective amount of the pharmaceuticalcomposition is administered. The cancer can include, e.g. breast, colon,ovarian, endometrial, gastric, pancreatic, prostate and salivary glandcancer. The administration of the pharmaceutical composition of theinvention can be by any of a variety of convenient methods including,e.g. systemic injectable administration, injection into a tumor orcancerous tissue, oral administration.

According to another embodiment the present invention provides a methodof treating a subject in need of protein replacement therapy comprisingadministering to a subject in need thereof a pharmaceutically effectiveamount of the pharmaceutical composition according to one or moreembodiments of the present invention or an effective amount of themodified mRNA, which has been modified in accordance to one or more ofthe embodiments of the inventive method.

The mode and method of administration and the dosage of thepharmaceutical composition according to the invention depends on severalfactors, such as e.g. on the nature of the disease to be cured, also thebody weight, the age and the sex of the patient and the route ofadministration of the inventive pharmaceutical composition.

The pharmaceutical composition according to the present inventioncomposition may be administered to an individual in need thereof, forexample, a patient, by any suitable administration route, such as byoral, topical, rectal, vaginal, dermal, intra-tumoural, nasal, lingual,parenteral administration or administration by inhalation, insufflation,injection, infusion or by enema. Thus, the modified mRNA obtainable byone or more embodiments of the inventive method for targeted modulationof the immunogenicity and/or immunostimulatory capacity of said mRNA,the pharmaceutical composition according to the present invention may beadapted, for example, for oral, topical, rectal, vaginal, dermal,intra-tumoural, nasal, lingual, parenteral administration oradministration by inhalation, insufflation, injection, infusion or byenema.

Furthermore, the method of treatment according to the present inventionmay comprise oral, topical, rectal, vaginal, dermal, intra-tumoural,nasal, lingual, parenteral administration or administration byinhalation, insufflation, injection, infusion or by enema. Preferredadministration routes are oral and parenteral administration, such asintravenous, intramuscular, subcutaneous, intranodal, intralymphatic,intra-tumoural or intraperitoneal injection or transdermal delivery.

More preferably, the present invention provides a method for expressinga biologically active peptide, polypeptide or protein in a tissue invivo, the method comprising contacting the patient with a pharmaceuticalcomposition according to one or more of the above embodiments of theinvention, or contacting the patient with the inventive modified mRNAaccording to any one of the above embodiments of the invention, whereinadministering the pharmaceutical composition or the modified mRNAresults in a reduced innate immune response by the patient relative to apatient contacted with the wild type mRNA molecule encoding the samepolypeptide or protein. Typically, the level of mRNA expression in vivois increased by the modified target mRNA of the invention as compared tothe wild type mRNA.

Further embodiments of the present invention are provided by the itemsas specified below:

item 22. Modified mRNA that codes for at least one biologically activepeptide polypeptide or protein, wherein

-   -   the cytosine-content of the coding region of the modified mRNA        is larger than the cytosine-content of the coding region of the        wild type mRNA coding for the polypeptide or protein whereby the        encoded amino acid sequence is unchanged compared to the wild        type sequence and optionally    -   if no cytosine is present in any of the at least one codon        coding for the amino acid, the at least one codon of the wild        type sequence that codes for a relatively rare tRNA in the cell        is exchanged for a codon that codes for a relatively frequent        tRNA in the cell that carries the same amino acid as the        relatively rare tRNA.

item 23. Modified mRNA according to item 22, wherein all codons of thewild type sequence, which code for a relatively rare codon in the cell,have been replaced by codons which code a relatively frequent tRNA inthe cell, which carries the same amino acid as the relatively rare tRNA.

item 24. Modified mRNA according to item 22 or item 23, wherein thecytosine-content of the polypeptide- or protein-coding region of themodified mRNA is at least 10%, preferably at least 12.5%, more preferredat least 15% greater than the cytosine content compared to thepolypeptide or protein coding region of the wild type mRNA.

item 25. Modified mRNA according to any one of items 22-24, wherein thecoding region of the modified mRNA is modified such that a maximalcytosine-content is achieved by means of codons which encode relativelyfrequent tRNAs.

item 26. Modified mRNA according to any one of items 22-25, wherein thecodon adaptation index (CAI) of the region coding for the polypeptide orprotein is greater by at least 0.05, preferably greater by at least 0.1,preferably greater by at least 0.125, more preferred greater by at least0.15 than the CAI of the wild type region of the mRNA coding for thepolypeptide or protein.

item 27. Modified mRNA according to any one of items 22-26, wherein thecoding region of the modified mRNA and/or the 5′ and/or 3′ untranslatedregion of the modified mRNA is changed in comparison to the polypeptide-or protein-encoding wildtype region such that no destabilizing elementsare present.

item 28. Modified mRNA according to any one of items 22-27, wherein themodified mRNA is characterized by having a 5′ CAP structure and/or apolyA-tail of at least 70 nucleotides and/or a 3′ stabilizing sequence.

item 29. Modified mRNA according to any one of items 22-28, wherein themodified mRNA coding for the polypeptide or protein is characterized bya lower binding affinity to mammalian cellular RNA sensors than the wildtype sequence coding for the polypeptide or protein, wherein themammalian cellular RNA sensors comprise one or more of TLR3, TLR7, TLR8,PKR, MDA5, RIG-I, LGP2, 2′-5′-oligoadenylate synthetase

item 30. Modified mRNA according to any one of items 22-29, wherein themodified mRNA encodes a polypeptide or protein for use in proteinreplacement therapy.

item 31. Modified mRNA according to any one of items 22-30, wherein themodified mRNA encodes for a polypeptide or protein selected from thegroup of α-glucosidase, acid β-glucosidase, α-galactosidase A,galactocerebrosidase Acid α-Mannosidase, Acid β-Mannosidase, Acidα-L-fucosidase, α-N-Acetylgalactosaminidase, β-Hexosaminidase A,β-Hexosaminidase B, α-L-Iduronidase, β-Glucuronidase, Sialidase,Iduronate sulfatase, Acid sphingomyelinase, pituitary-related growthhormone, growth hormone releasing hormone (GHRH), erythropoetin, orthyroid stimulating hormone.

item 32. Modified mRNA according to any one of items 22-31, for use inprotein replacement therapy.

item 33. Kit of parts for use in aiding in protein replacement therapy,wherein the kit comprises

-   -   (i) the isolated and purified mRNA according to any one of items        22-31,    -   (ii) means for applying the mRNA to an individual, e.g. a human.

Sequence Listing SEQ ID NO: 1 R873, Photinus pyralis luciferase wildtype mRNA SEQ ID NO: 2 R875, G/C-enriched mRNA sequence SEQ ID NO: 3R2103, C-enriched mRNA sequence SEQ ID NO: 4 R2349, G/C-enriched mRNAsequence SEQ ID NO: 5 R2350, C-optimized mRNA sequence SEQ ID NO: 6R2791, G/C-enriched mRNA sequence SEQ ID NO: 7 R2793, C-optimized mRNAsequence

EXAMPLES Example 1 Preparation of mRNA

Preparation of DNA and mRNA Constructs

For the present examples DNA sequences encoding the Photinus pyralisluciferase were prepared and used for subsequent in vitro transcriptionreactions.

According to a first preparation, the DNA sequences coding for the mRNAsshown in Table 1 were prepared.

The G/C-enriched sequences of the examples provided were obtainedaccording to the method as disclosed in WO2002098443 A2. The C-enrichedmodified mRNA coding region was obtained by the method of the presentinvention. However, alternatively, the C-enriched mRNA of the examplesincluded may also be obtained according to the alternative embodiment asdisclosed above, i.e. in a first step, the G/C content may be increased,e.g. by substituting wild type codons exhibiting a lower content of Gand C nucleotides as disclosed in WO2002098443 A2. As a second step theG/C-enrichment or maximization is followed by a step of furtherC-optimization.

A vector for in vitro transcription was constructed containing a T7promoter followed by a sequence coding for Photinus pyralis luciferase(PpLuc(wt), obtained from Promega) and a poly(A) sequence of 70adenosine nucleotides (A70 poly(A) sequence). mRNA obtained from thisvector by in vitro transcription is designated as “PpLuc(wt)-A70”(R873). In FIG. 1 (SEQ ID NO: 1) the sequence of the corresponding wildtype luciferase mRNA is shown.

The vector was modified by replacing the wild type coding sequence ofthe mRNA by a GC-enriched (R875, FIG. 2, SEQ ID NO:2) or C-enriched(R2103, FIG. 3, SEQ ID NO:3) coding sequence, respectively, forstabilization. mRNA was obtained from these vectors by in vitrotranscription.

A further vector for in vitro transcription was constructed containing aT7 promoter followed by a GC-enriched sequence coding for Photinuspyralis luciferase (PpLuc(GC)III) and an A64 poly(A) sequence. Thevector was modified by replacing the GC-optimized coding sequence by aC-enriched sequence.

mRNA obtained from these vectors by in vitro transcription is designatedas “PpLuc(GC)III-A64” (R2349) or PpLuc(GC)V-A64 (R2350), respectively.

In SEQ ID NO: 4 (FIG. 4) and SEQ ID NO: 5 (FIG. 5) the sequences of thecorresponding mRNAs are shown.

Two further vectors were prepared by introducing a 5′-TOP-UTR derivedfrom the ribosomal protein 32L, modifying the wild type coding sequenceby introducing a GC-optimized or C-optimized sequence for stabilization,followed by a stabilizing sequence derived from the albumin-3′-UTR, astretch of 64 adenosines (poly(A)-sequence), a stretch of 30 cytosines(poly(C)-sequence), and a histone stem loop. mRNA obtained from thesevectors by in vitro transcription is designated as R2791 or R2793,respectively. In SEQ ID NO: 6 (FIG. 6) and SEQ ID NO: 7 (FIG. 7) thesequences of the corresponding mRNAs are shown.

TABLE 1 Luciferase mRNA constructs Composition of R SEQ ID complete RNAnumber NO. Construct Base Number % R873 SEQ ID ppLuc(wt) . . . A70 A 53430.4 NO. 1 C 371 21.1 G 418 23.8 T 435 24.7 R875 SEQ ID ppLuc(GC)II . .. A70 A 405 23.0 NO. 2 C 579 32.9 G 517 29.4 T 257 14.6 R2103 SEQ IDppLuc(GC)V . . . A70 A 390 22.2 NO. 3 C 710 40.4 G 386 22.0 T 272 15.5R2349 SEQ ID PpLuc(GC)III . . . A64 A 397 22.7 NO. 4 C 600 34.4 G 49228.2 T 257 14.7 R2350 SEQ ID PpLuc(GC)V . . . A64 A 382 21.9 NO. 5 C 70940.6 G 385 22.1 T 270 15.5 R2791 SEQ ID 32L4 . . . PpLuc(GC)II . . . A476 23.4 NO. 6 albumin7 . . . A64 . . . C C 668 32.8 30-histoneSL-N5 G556 27.3 T 335 16.5 R2793 SEQ ID 32L4 . . . PpLuc(GC)V . . . A 461 22.7NO. 7 albumin7 . . . A64 . . . C C 799 39.3 30-histoneSL-N5 G 425 20.9 T350 17.2

2. In Vitro Transcription

The respective DNA plasmids prepared according to paragraph 1 weretranscribed in vitro using T7 polymerase in the presence of a CAP analog(m⁷GpppG). Subsequently the mRNA was purified using PureMessenger®(CureVac, Tubingen, Germany; WO2008/077592A1).

3. Reagents

Complexation Reagent: protamine

4. Formulation of mRNA

The mRNA was complexed with protamine by addition of protamine to themRNA in the ratio RNA/protamine of 2:1 (w/w).

Example 2 Immunostimulation of Peripheral Blood Mononuclear Cells(PBMCs) Treated with Modified mRNAs

Preparation of Human PBMCs

25 ml of a buffy coat were layered over 20 ml of Ficoll in a 50 mlFalcon tube. After centrifugation at 805 relative centrifugal force(rcf) for 20 minutes, cells at the interphase were collected. Cells werewashed two times by resuspending in PBS and centrifuging. Aftercounting, cells were resuspended at 50 million cells per ml in fetalcalf serum, 10% DMSO, and frozen.

PBMC Stimulation

Human PBMCs were seeded at a density of 10⁶ cells/ml into each well of a96-well plate (2×10⁵ cells/well) in X-Vivo 15 medium (Lonza) and treatedwith 10 μg/ml of GC- or C-enriched mRNA for 20 hours and the TNFαconcentration was determined in the supernatant by ELISA.

Cytokine ELISA (TNFα)

96 well ELISA plates were coated with capture antibody (BD Pharmingen)in coating buffer (15 mM Na₂CO₃, 15 mM NaHCO₃, 0.02% NaN₃, pH 9.6) overnight at room temperature. Plates were blocked with blocking buffer(PBS, 0.05% Tween-20, 1% BSA, pH7.4) for 1 hour at room temperature.Plates were washed three times (PBS, 0.05% Tween-20, pH7.4). 50 μl ofsupernatants of stimulated PBMC, diluted with 50 μl of blocking buffer,were added to the plates and incubated for 2 hours at room temperature.Plates were washed three times. Biotinylated detection antibody dilutedin blocking buffer was added to the plates and incubated for 1 hour atroom temperature. Plates were washed three times. HRP-Streptavidindiluted in blocking buffer without NaN₃ was added to the plates andincubated for 30 minutes at room temperature. Plates were washed threetimes. 100 μl/well of TMB substrate (Perbioscience) was added to theplates. To stop color development, 100 μl of 20% H₂SO₄ was added to theplates. Absorbance at 450 nm was measured.

Transfection of HeLa Cells and Determination of Luciferase Activity

HeLa cells were trypsinized and washed in opti-MEM medium (LifeTechnologies). Cells were electroporated with PpLuc-encoding mRNA in 200μl volume. Electroporated cells were seeded in 24-well plates in 1 ml ofRPMI 1640 medium (between 0.3 to 0.5 μg of PpLuc mRNA and 100000 cellsper well). 6, 24, or 48 hours after transfection, medium was aspiratedand cells were lysed. Lysates were stored at −80° C. Luciferase activitywas measured as relative light units (RLU) in a BioTek SynergyHT platereader. PpLuc activity was measured at 5 seconds measuring time using 50μl of lysate and 200 p.I of luciferin buffer (75 μM luciferin, 25 mMGlycylglycin, pH 7.8 (NaOH), 15 mM MgSO₄, 2 mM ATP).

Results

FIG. 8 shows that the treatment of human PBMCs with C-enriched mRNA(R2793) results in significantly less TNFα secretion compared totreatment with GC-enriched mRNA (R2791).

FIG. 9A shows that the activity of luciferase encoded by GC-enrichedmRNA (R875) and C-enriched mRNA (R2103) was comparable both in terms ofpeak level and kinetics.

FIG. 9B shows that the activity of luciferase encoded by GC-enrichedmRNA (R875) was much higher than that of the wildtype construct (R873).

Example 3 Dose-Response Relationship for Immunostimulation of PBMCsTreated with Modified mRNAs

PBMC Stimulation

Human PBMCs were prepared as described in Example 2.PBMCs were seeded ata density of 10⁶ cells/ml into each well of a 96-well plate (2×10⁵cells/well) in X-Vivo 15 medium (Lonza) and treated with 40 or 20 μg/mlof GC- or C-enriched mRNAs as indicated for 20 hours. The TNFα andIFNαconcentrations were determined in the supernatant by ELISA.

Cytokine ELISA

The TNFα ELISA was performed as described in Example 2. The IFNα ELISAwas performed analogously, replacing the capture and detectionantibodies appropriately (Mabtech).

Results

FIG. 10 shows the dose-response relationship for TNFα secretion of humanPBMCs treated with various modified mRNAs. As can be seen the treatmentwith C-enriched mRNA results in less TNFα secretion than withGC-enriched mRNA.

FIG. 11 shows the dose-response relationship for IFNα secretion of humanPBMCs treated with various modified mRNAs. As can be seen the treatmentwith C-enriched mRNA results in less TNFα secretion than withGC-enriched mRNA.

TABLE 2 Summary of the nucleotide composition and codon usage of theconstructs used in the present Examples ppLuc(GC) PpLuc(wt) G: 542 G:410 A: 333 A: 454 T: 240 T: 426 C: 538 C: 363 Seltene Seltene Codons: 41Codons: 45 human Codon-usage GC-reicher Code CAI: 0.185 CAI: 0.222 AAcod frac /1000 AA cod frac cod number frac cod number frac Ala GCG 0.107.4 Ala GCG 0.20 GCG 7.00 0.16 GCG 11 2.0 Ala GCA 0.22 15.8 Ala GCA 0.00GCA 0.00 0.00 GCA 7 1.3 Ala GCT 0.28 18.5 Ala GCT 0.00 GCT 0.00 0.00 GCT12 2.2 Ala GCC 0.40 27.7 Ala GCC 0.80 GCC 36.00 0.84 GCC 13 2.4 Cys TGT0.42 10.6 Cys TGT 0.00 TGT 0.00 0.00 TGT 2 0.4 Cys TGC 0.58 12.6 Cys TGC1.00 TGC 4.00 1.00 TGC 2 0.4 Asp GAT 0.44 21.8 Asp GAT 0.00 GAT 0.000.00 GAT 17 3.1 Asp GAC 0.56 25.1 Asp GAC 1.00 GAC 32.00 1.00 GAC 15 2.7Glu GAG 0.59 39.6 Glu GAG 1.00 GAG 33.00 1.00 GAG 10 1.8 Glu GAA 0.4129.0 Glu GAA 0.00 GAA 0.00 0.00 GAA 23 4.2 Phe TTT 0.43 17.6 Phe TTT0.00 TTT 0.00 0.00 TTT 15 2.7 Phe TTC 0.57 20.3 Phe TTC 1.00 TTC 30.001.00 TTC 15 2.7 Gly GGG 0.23 16.5 Gly GGG 0.41 GGG 8.00 0.17 GGG 6 1.1Gly GGA 0.26 16.5 Gly GGA 0.00 GGA 0.00 0.00 GGA 17 3.1 Gly GGT 0.1810.8 Gly GGT 0.00 GGT 0.00 0.00 GGT 13 2.4 Gly GGC 0.33 22.2 Gly GGC0.59 GGC 38.00 0.83 GGC 10 1.8 His CAT 0.41 10.9 His CAT 0.00 CAT 0.000.00 CAT 8 1.5 His CAC 0.59 15.1 His CAC 1.00 CAC 14.00 1.00 CAC 6 1.1Ile ATA 0.14 7.5 Ile ATA 0.00 ATA 0.00 0.00 ATA 4 0.7 Ile ATT 0.35 16.0Ile ATT 0.00 ATT 0.00 0.00 ATT 18 3.3 Ile ATC 0.52 20.8 Ile ATC 1.00 ATC39.00 1.00 ATC 17 3.1 Lys AAG 0.60 31.9 Lys AAG 1.00 AAG 39.00 1.00 AAG19 3.5 Lys AAA 0.40 24.4 Lys AAA 0.00 AAA 0.00 0.00 AAA 20 3.6 Leu TTG0.12 12.9 Leu TTG 0.00 TTG 0.00 0.00 TTG 11 2.0 Leu TTA 0.06 7.7 Leu TTA0.00 TTA 0.00 0.00 TTA 5 0.9 Leu CTG 0.43 39.6 Leu CTG 0.68 CTG 42.000.82 CTG 19 3.5 Leu CTA 0.07 7.2 Leu CTA 0.00 CTA 0.00 0.00 CTA 3 0.5Leu CTT 0.12 13.2 Leu CTT 0.00 CTT 0.00 0.00 CTT 5 0.9 Leu CTC 0.20 19.6Leu CTC 0.32 CTC 9.00 0.18 CTC 8 1.5 Met ATG 1.00 22.0 Met ATG 1.00 ATG14.00 1.00 ATG 14 2.5 Asn AAT 0.44 17.0 Asn AAT 0.00 AAT 0.00 0.00 AAT 81.5 Asn AAC 0.56 19.1 Asn AAC 1.00 AAC 17.00 1.00 AAC 9 1.6 Pro CCG 0.116.9 Pro CCG 0.25 CCG 24.00 0.83 CCG 7 1.3 Pro CCA 0.27 16.9 Pro CCA 0.00CCA 0.00 0.00 CCA 7 1.3 Pro CCT 0.29 17.5 Pro CCT 0.00 CCT 0.00 0.00 CCT7 1.3 Pro CCC 0.33 19.3 Pro CCC 0.75 CCC 5.00 0.17 CCC 8 1.5 Gln CAG0.73 34.2 Gln CAG 1.00 CAG 16.00 1.00 CAG 5 0.9 Gln CAA 0.27 12.3 GlnCAA 0.00 CAA 0.00 0.00 CAA 11 2.0 Arg AGG 0.22 12.0 Arg AGG 0.00 AGG0.00 0.00 AGG 4 0.7 Arg AGA 0.21 12.1 Arg AGA 0.00 AGA 0.00 0.00 AGA 101.8 Arg CGG 0.19 11.4 Arg CGG 0.50 CGG 16.00 0.80 CGG 1 0.2 Arg CGA 0.106.2 Arg CGA 0.00 CGA 0.00 0.00 CGA 2 0.4 Arg CGT 0.09 4.5 Arg CGT 0.00CGT 0.00 0.00 CGT 1 0.2 Arg CGC 0.19 10.4 Arg CGC 0.50 CGC 4.00 0.20 CGC2 0.4 Ser AGT 0.14 12.1 Ser AGT 0.00 AGT 0.00 0.00 AGT 5 0.9 Ser AGC0.25 19.5 Ser AGC 0.52 AGC 23.00 0.82 AGC 2 0.4 Ser TCG 0.06 4.4 Ser TCG0.00 TCG 5.00 0.18 TCG 3 0.5 Ser TCA 0.15 12.2 Ser TCA 0.00 TCA 0.000.00 TCA 1 0.2 Ser TCT 0.18 15.2 Ser TCT 0.00 TCT 0.00 0.00 TCT 10 1.8Ser TCC 0.23 17.7 Ser TCC 0.48 TCC 0.00 0.00 TCC 7 1.3 Thr ACG 0.12 6.1Thr ACG 0.24 ACG 5.00 0.17 ACG 5 0.9 Thr ACA 0.27 15.1 Thr ACA 0.00 ACA0.00 0.00 ACA 9 1.6 Thr ACT 0.23 13.1 Thr ACT 0.00 ACT 0.00 0.00 ACT 81.5 Thr ACC 0.38 18.9 Thr ACC 0.76 ACC 24.00 0.83 ACC 7 1.3 Val GTG 0.4828.1 Val GTG 0.66 GTG 37.00 0.82 GTG 15 2.7 Val GTA 0.10 7.1 Val GTA0.00 GTA 0.00 0.00 GTA 4 0.7 Val GTT 0.17 11.0 Val GTT 0.00 GTT 0.000.00 GTT 17 3.1 Val GTC 0.25 14.5 Val GTC 0.34 GTC 8.00 0.18 GTC 9 1.6Trp TGG 1.00 13.2 Trp TGG 1.00 TGG 2.00 1.00 TGG 2 0.4 Tyr TAT 0.42 12.2Tyr TAT 0.00 TAT 0.00 0.00 TAC 11 2.0 Tyr TAC 0.58 15.3 Tyr TAC 1.00 TAC19.00 1.00 TAT 8 1.5 Stop TGA 0.61 1.6 End TGA 0.78 TGA 0.00 0.00 TAA 1Stop TAG 0.17 0.8 End TAG 0.22 TAG 0.00 0.00 Stop TAA 0.22 1.0 End TAA0.00 TAA 1.00 1.00 ppLuc(GC)II ppLuc(GC)III ppLuc(GC)V G: 507 G: 483 G:376 A: 324 A: 324 A: 309 T: 249 T: 251 T: 264 C: 573 C: 595 C: 704Seltene Seltene Seltene Codons: 24 Codons: 0 Codons: 0 CAI: 0.193 CAI:0.190 CAI: 0.385 cod number frac cod number frac cod num frac GCG 9.000.21 GCG 0.00 0.00 GCG 0 0.00 GCA 0.00 0.00 GCA 0.00 0.00 GCA 0 0.00 GCT0.00 0.00 GCT 0.00 0.00 GCT 0 0.00 GCC 34.00 0.79 GCC 43.00 1.00 GCC 431.00 TGT 0.00 0.00 TGT 0.00 0.00 TGT 0 0.00 TGC 4.00 1.00 TGC 4.00 1.00TGC 4 1.00 GAT 0.00 0.00 GAT 0.00 0.00 GAT 0 0.00 GAC 32.00 1.00 GAC32.00 1.00 GAC 32 1.00 GAG 33.00 1.00 GAG 33.00 1.00 GAG 33 1.00 GAA0.00 0.00 GAA 0.00 0.00 GAA 0 0.00 TTT 0.00 0.00 TTT 0.00 0.00 TTT 00.00 TTC 30.00 1.00 TTC 30.00 1.00 TTC 30 1.00 GGG 19.00 0.41 GGG 19.000.41 GGG 0 0.00 GGA 0.00 0.00 GGA 0.00 0.00 GGA 0 0.00 GGT 0.00 0.00 GGT0.00 0.00 GGT 0 0.00 GGC 27.00 0.59 GGC 27.00 0.59 GGC 46 1.00 CAT 0.000.00 CAT 0.00 0.00 CAT 0 0.00 CAC 14.00 1.00 CAC 14.00 1.00 CAC 14 1.00ATA 0.00 0.00 ATA 0.00 0.00 ATA 0 0.00 ATT 0.00 0.00 ATT 0.00 0.00 ATT 00.00 ATC 39.00 1.00 ATC 39.00 1.00 ATC 39 1.00 AAG 39.00 1.00 AAG 39.001.00 AAG 39 1.00 AAA 0.00 0.00 AAA 0.00 0.00 AAA 0 0.00 TTG 0.00 0.00TTG 0.00 0.00 TTG 0 0.00 TTA 0.00 0.00 TTA 0.00 0.00 TTA 0 0.00 CTG34.00 0.67 CTG 34.00 0.67 CTG 0 0.00 CTA 0.00 0.00 CTA 0.00 0.00 CTA 00.00 CTT 0.00 0.00 CTT 0.00 0.00 CTT 0 0.00 CTC 17.00 0.33 CTC 17.000.33 CTC 51 1.00 ATG 14.00 1.00 ATG 14.00 1.00 ATG 14 1.00 AAT 0.00 0.00AAT 0.00 0.00 AAT 0 0.00 AAC 17.00 1.00 AAC 17.00 1.00 AAC 17 1.00 CCG8.00 0.28 CCG 0.00 0.00 CCG 0 0.00 CCA 0.00 0.00 CCA 0.00 0.00 CCA 00.00 CCT 0.00 0.00 CCT 2.00 0.07 CCT 0 0.00 CCC 21.00 0.72 CCC 27.000.93 CCC 29 1.00 CAG 16.00 1.00 CAG 16.00 1.00 CAG 16 1.00 CAA 0.00 0.00CAA 0.00 0.00 CAA 0 0.00 AGG 0.00 0.00 AGG 0.00 0.00 AGG 0 0.00 AGA 0.000.00 AGA 0.00 0.00 AGA 0 0.00 CGG 10.00 0.50 CGG 10.00 0.50 CGG 0 0.00CGA 0.00 0.00 CGA 0.00 0.00 CGA 0 0.00 CGT 0.00 0.00 CGT 0.00 0.00 CGT 00.00 CGC 10.00 0.50 CGC 10.00 0.50 CGC 20 1.00 AGT 0.00 0.00 AGT 0.000.00 AGT 0 0.00 AGC 15.00 0.54 AGC 15.00 0.54 AGC 0 0.00 TCG 0.00 0.00TCG 0.00 0.00 TCG 0 0.00 TCA 0.00 0.00 TCA 0.00 0.00 TCA 0 0.00 TCT 0.000.00 TCT 0.00 0.00 TCT 0 0.00 TCC 13.00 0.46 TCC 13.00 0.46 TCC 28 1.00ACG 7.00 0.24 ACG 0.00 0.00 ACG 0 0.00 ACA 0.00 0.00 ACA 0.00 0.00 ACA 00.00 ACT 0.00 0.00 ACT 0.00 0.00 ACT 0 0.00 ACC 22.00 0.76 ACC 29.001.00 ACC 29 1.00 GTG 29.00 0.64 GTG 29.00 0.64 GTG 0 0.00 GTA 0.00 0.00GTA 0.00 0.00 GTA 0 0.00 GTT 0.00 0.00 GTT 0.00 0.00 GTT 0 0.00 GTC16.00 0.36 GTC 16.00 0.36 GTC 45 1.00 TGG 2.00 1.00 TGG 2.00 1.00 TGG 21.00 TAT 1.00 0.05 TAT 1.00 0.05 TAT 1 0.05 TAC 18.00 0.95 TAC 18.000.95 TAC 18 0.95 TGA 1.00 1.00 TGA 1.00 1.00 TGA 1 1.00 TAG 0.00 0.00TAG 0.00 0.00 TAG 0 0.00 TAA 0.00 0.00 TAA 0.00 0.00 TAA 0 0.00

1. Method for targeted modulation of an immune response against an mRNAcoding for at least one biologically active polypeptide or protein,wherein the method comprises the steps of (1) identifying a target mRNAwild type sequence coding for the biologically active polypeptide orprotein and modifying at least 70% of the codons of the wild typesequence which are cytosine content optimizable by increasing thecytosine-content of the mRNA such that the cytosine-content of thecoding region of the modified mRNA is larger than the cytosine-contentof the coding region of the wild type mRNA, whereby the amino acidsequence encoded by the modified RNA is unchanged compared to the wildtype or reference sequence.
 2. Method according to claim 1, wherein thecoding region of the target mRNA is modified such that a maximalcytosine-content is achieved by introduction of codons, which recognizerelatively frequent tRNAs.
 3. Method according to claim 1, wherein thecytosine-content of the region of the modified mRNA coding for at leastone the polypeptide or protein is at least 10%.
 4. Method according toclaim 1, wherein all codons of the wild type sequence, which are notcytosine-content optimizable and which code for a relatively rare codonin the cell have been replaced by codons which code for a relativelyfrequent tRNA in the cell, which carries the same amino acid as therelatively rare tRNA.
 5. Method according to claim 1, wherein the codonadaptation index (CAI) of the coding region of the modified target mRNAis greater by at least 0.05.
 6. Method according to claim 1, wherein themethod further comprises the step of determining the immunogenicityand/or immunostimulatory capacity of the modified target mRNA coding forthe at least one polypeptide or protein.
 7. Method according to claim 1,wherein determining the immunogenicity and/or immunostimulatory capacityof the modified target mRNA comprises the sub-steps of (i) transfectingPBMC with the modified mRNA, (ii) cultivating the cells for anappropriate amount of time, (iii) measuring the amount ofpro-inflammatory cytokines in the cell supernatant.
 8. Method accordingto claim 1, wherein the target mRNA of lower immunogenicity and/orimmunostimulatory capacity coding for the polypeptide or protein isselected, optionally the method is reiterated to further decrease theimmunogenicity and/or immunostimulatory capacity of the target mRNA. 9.Method according to claim 1, wherein the method of targeted modulationof the immune response against a target mRNA encoding at least onebiologically active polypeptide or protein is carried out by way ofexecuting at least one algorithm on a computer with the aid of suitablesoftware.
 10. Method according to claim 1, wherein the modified targetmRNA is obtained by synthesis.
 11. Method according to claim 1, whereinthe modified target mRNA is obtained by in vitro transcription. 12.Modified target mRNA encoding at least one biologically activepolypeptide or protein obtainable by a method of claim 1 having reducedimmunogenicity and/or immunostimulatory capacity compared to the wildtype target mRNA.
 13. Modified target mRNA according to claim 12,wherein the modified target mRNA is characterized by a lower affinity toone or more of TLR3, TLR7, TLR8, PKR, MDA5, RIG-I, LGP2 or2′-5′-oligoadenylate synthetase compared to the wild type target mRNAencoding the at least one biologically active polypeptide or protein.14. Modified target mRNA according to claim 12, wherein the modifiedtarget mRNA is devoid of destabilising sequence elements (DSE) in the 3′and/or 5′ UTR.
 15. Modified target mRNA according to claim 12, whereinthe modified target mRNA further comprises a 5′ CAP structure and/or apolyA-tail of at least 60 nucleotides, preferably of at least 70nucleotides and/or a 3′ stabilizing sequence.
 16. Pharmaceuticalcomposition comprising the modified target mRNA obtainable by a methodof claim
 1. 17. Pharmaceutical composition according to claim 16 for usein the treatment of protein deficiency disorders by protein replacementtherapy.
 18. (canceled)
 19. Method of treating a subject in need ofprotein replacement therapy comprising administering to a subject inneed thereof a pharmaceutically effective amount of the pharmaceuticalcomposition according to claim
 16. 20. Method according to claim 19,wherein the disease to be treated by protein replacement therapy isselected from the group consisting of hereditary or endocrinologicaldiseases, wherein the group comprises amino acid metabolism disorders,carbohydrate metabolism disorders, cholesterol biosynthesis disorders,fatty acid oxidation defects and fat metabolism disorders, lacticacidosis, glycogen storage diseases, mitochondrial disorders, organicacid disorders, urea cycle disorders, vitamin/cofactor disorders,lysosomal storage disease disorders.
 21. Method for expressing abiologically active polypeptide or protein in a tissue in vivo, themethod comprising contacting the patient with the pharmaceuticalcomposition according to claim 16, wherein administering thepharmaceutical composition or the modified target mRNA results in areduced innate immune response by the patient relative to a patientcontacted with the wild type target mRNA molecule encoding the samepolypeptide or protein, wherein the level of mRNA expression in vivo ispreferably increased by the modified target mRNA of the invention ascompared to the wild type target mRNA.